Forward Looking Statements 2022 Aeglea BioTherapeutics. External 2 This presentation and the accompanying oral presentation contain "forward-looking" statements that are based on our management's beliefs and assumptions

Reimagining The Potential Of Human Enzyme Therapeutics Corporate Overview - January 2022 Nasdaq: AGLE Exhibit 99.1

Forward Looking Statements 2022 Aeglea BioTherapeutics. External 2 This presentation and the accompanying oral presentation contain "forward-looking" statements that are based on our management's beliefs and assumptions and on information currently available to management. Forward-looking statements include all statements other than statements of historical fact contained in this presentation, including information concerning our current and future financial performance, business plans and objectives, current and future clinical and preclinical development activities, timing and success of our ongoing and planned clinical trials and related data, the timing of announcements, updates, results of our clinical trials and related data and our planned BLA submission for our lead product candidate pegzilarginase, our ability to obtain and maintain regulatory approval, the potential therapeutic benefits, safety profile and economic value of pegzilarginase and our other product candidates, potential growth opportunities, financing plans, use and adequacy of financing plans, competitive position, industry environment and potential market opportunities.

Forward-looking statements are subject to known and unknown risks, uncertainties, assumptions and other factors including, but not limited to, those related to the success, cost and timing of our product candidate development activities and ongoing and planned clinical trials; our plans to develop and commercialize targeted therapeutics, including our lead product candidate pegzilarginase and our product candidates for the treatment of homocystinuria and cystinuria; the design, progress of patient enrollment and dosing in our clinical trials; the ability of our product candidates to achieve applicable endpoints in clinical trials; the safety profile of our product candidates in clinical trials; the potential for data from our current and future clinical trials to support a marketing application, as well as the timing of these events; the potential for preclinical studies to be predictive of current or future clinical trials; our ability to obtain funding for our operations, development and commercialization of our product candidates; the impact of the COVID-19 pandemic on our operations and clinical development activities, including on the timing of enrollment of our clinical trials; the timing of and our ability to obtain and maintain regulatory approvals; our ability to obtain regulatory approval for, and commercialize, pegzilarginase, and recognize milestone and royalty payments from our licensing and supply agreement with Immedica; the potential for expedited development and review of pegzilarginase as a result of its Breakthrough Therapy designation; the potential addressable markets of our product candidates; the rate and degree of market acceptance and clinical utility of our product candidates; the size and growth potential of the markets for our product candidates, and our ability to serve those markets; our commercialization, marketing and manufacturing capabilities and strategy; future agreements with third parties in connection with the potential commercialization of our product candidates; our expectations regarding our ability to obtain and maintain intellectual property protection; our dependence on third party manufacturers; our ability to develop our own commercial manufacturing facility; the success of competing therapies that are or may become available; our ability to attract and retain key scientific or management personnel; our ability to identify additional product candidates with significant commercial potential consistent with our commercial objectives; and our estimates regarding expenses, future revenue, capital requirements and needs for additional financing.

Moreover, we operate in a very competitive and rapidly changing environment, and new risks may emerge from time to time. It is not possible for our management to predict all risks, nor can we assess the impact of all factors on our business or the extent to which any factor, or combination of factors, may cause actual results to differ materially from those contained in any forward-looking statements we may make. In light of these risks, uncertainties and assumptions, the forward-looking events and circumstances discussed herein may not occur and actual results could differ materially and adversely from those anticipated or implied in the forward-looking statements. Further information on these and other factors that could affect these forward-looking statements is contained in our most recent Quarterly Report on Form 10-Q filed with the U.S. Securities and Exchange Commission (SEC) and other reports filed by the SEC. You should not rely upon forward-looking statements as predictions of future events. Although our management believes that the expectations reflected in our forward-looking statements are reasonable, we cannot guarantee that the future results, levels of activity, performance or events and circumstances described in the forward-looking statements will be achieved or occur. We undertake no obligation to publicly update any forward-looking statements, whether written or oral, that may be made from time to time, whether as a result of new information, future developments or otherwise.

Addressing Metabolic Imbalances to Improve the Lives of Patients 2022 Aeglea BioTherapeutics. External 3 Aeglea BioTherapeutics

At Aeglea, we believe that every patient deserves a chance at a better life. We are committed to helping people with rare and devastating metabolic diseases who have limited treatment options. Having a rare disease does not mean that you are in the fight alone.

Looking Ahead to 2022 Key 2021 Highlights 4 Pegzilarginase

File U.S. BLA (1H 2022) and EU MAA

Continue preparations for strong, rapid launch in U.S., Europe and Middle East

Presentation of PEACE data at upcoming key metabolic conference; publication of long-term data

Clinical data from Phase 1/2 trial

AGLE-325 (Cystinuria)

IND-enabling studies for optimized molecule 2021 Accomplishments and 2022 Outlook Pegzilarginase (Arginase 1 Deficiency)

Signed license and supply agreement with Immedica Pharma AB for Europe and certain Middle Eastern countries

Announced positive topline Phase 3 data

Reduced arginine by 80%; normalized plasma arginine levels in 90.5% of patients; trend in mobility measure

Progressed key launch objectives including:

Patient identification and profiling of population and prescriber base; payer engagement; advancing patient services and distribution activities

AGLE-177 (Homocystinuria)

Began dosing patients in Phase 1/2 study

Advanced manufacturing and formulation work to enable Phase 3 trial

Competed long term toxicology studies 2022 Aeglea BioTherapeutics. External

5 Aeglea's Human Enzyme Platform for Rare Metabolic Diseases 1 Ex-U.S. license and supply agreement with Immedica to commercialize pegzilarginase in Europe and certain countries in the Middle East (European Economic Area, United Kingdom, Switzerland, Andorra, Monaco, San Marino, Vatican City, Turkey, Saudi Arabia, United Arab Emirates, Qatar, Kuwait, Bahrain and Oman) 2 ARG1-D case reports ; Diez-Fernandez et al. Mutations and common variants in the human arginase 1 (ARG1) gene: impact on patients, diagnostics and protein structure considerations. Hum Mutat. 2018 Aug;39(8):1029-10502. 3 >30,000 represents estimated prevalence of Classical Homocystinuria in 38 addressable markets based on results of U.S. ICD-10 claims analysis extrapolated to global markets; all figures rounded. Sellos-Moura et al 2020 4 Castro Pereira DJ et al 2015; Leslie and Nazzal Renal Calculi (Cystinuria, Cystine Stones) (2018) Reference; Rozanski et al, Mil Med (2005); Soucie et al, JM Kidney Int (1994); Claes & Jackson, Pediatr Nephrol (2012) 27, 2031; Chillaro n, J. et al. Nat. Rev. Nephrol. 2010, 6, 7, 424-34; Biyani, C.S and Cartledge, J.J. EAU-EBU Update Series, 2006, 4, 175-183; Mattoo, A. and Goldfarb D.S. 2008 Sem. Nephrol, 28, 2, 181-191 2022 Aeglea BioTherapeutics. External

Pegzilarginase for Arginase 1 Deficiency

The Progressive Impact of Persistently High Plasma Arginine1-4 Arginase 1 Deficiency (ARG1-D) Disease Overview 7 Infancy2-4,7,8

Initial 6-12 months may be uneventful

May present with seizures, episodes of hyperammonemia: irritability, feeding difficulties, poor appetite, nausea/vomiting, decreased alertness

Toddlerhood (2-4 years) 2,3,7-9

Spasticity in lower limbs (tiptoe walking)

Seizures, avoidance of protein is common and intellectual disability Childhood (5-10 years) 2,3,5,6,9

Progressive spasticity and growth impairment

Declining neuromotor and intellectual capabilities

Increasing dependence on walking aids

Decrease/loss of vocabulary/language

Adolescence (11-17 years)2,3,5,10

Potential loss of ambulation and bowel/bladder control

Severe intellectual disability Adulthood (18+ years) 2,3,11,12

Continued decline with increasing disability that may result in early mortality 1 Diez-Fernandez C, et al. Hum Mutat. 2018;39:1029-1050. 2 Carvalho DR, et al. Pediatr Neurol. 2012;46:369-374. 3 Crombez EA, Cederbaum SD. Mol Genet Metab. 2005;84:243-251. 4 De Deyn PP, et al. Hyperargininemia: a treatable inborn error of metabolism. In: Guanidino Compounds in Biology and Medicine. London, UK: John Libbey Company Ltd.; 1997:53-69. 5 Prasad A, et al. J Child Neurol. 1997;12:301-309. 6 Amayreh W, et al. Dev Med Child Neurol. 2014;56:1021-1024. 7 Scaglia F, Lee B. Am J Med Genet C Semin Med Genet. 2006;142C:113-120. 8 Sin YY, et al. J Mol Med (Berl). 2015;93:1287-1296. 9 Cai X, et al. Medicine (Baltimore). 2018;97:e9880. 10 Schlune A, et al. J. Amino Acids. 2015;47:1751-1762. 11 Sun A, et al. Arginase deficiency. In: Adam MP, et al, eds. GeneReviews . Seattle, WA: University of Washington, Seattle; 2020. 12 Diaz GA, et al. Poster presented at: 13th European Paediatric Neurology Society (EPNS) Congress; September 17-21, 2019; Athens, Greece. Poster P06-34. Current Standard of Care

Focused on lowering plasma arginine levels and controlling hyperammonemia with:

Severe dietary protein restriction

Amino acid supplementation

Ineffective at controlling plasma arginine levels

Significant Unmet Need

High arginine levels

Severe and progressive disease with early mortality

Easily diagnosed but often missed due to lack of awareness

No approved therapies to address high arginine levels

ARG1-D is a serious, progressive disease with early mortality and high unmet medical need. It is caused by a mutation in the arginase 1 enzyme, resulting in persistently high levels of arginine. 2022 Aeglea BioTherapeutics. External

8 Pegzilarginase Program Overview Commercial Opportunity

>2,500 patients in global addressable markets

>1,150 patients in territories with regulatory and launch plans underway

High unmet medical need

No approved therapies to address high arginine levels

Regulatory Designations

U.S. Rare Pediatric Disease (PRV eligible)

Breakthrough Therapy

Pegzilarginase is a novel recombinant human enzyme engineered to lower arginine levels. Planned BLA Filing in First Half of 2022 Phase 1/2 and Open-Label Extension Trials

13 patients remain on therapy from 2-4 years

Arginine lowering was rapid and durable

Improvements in functional measures sustained over time

PEACE Phase 3 Clinical Trial

First placebo-controlled trial ever conducted in ARG1-D

Topline announced December 2021

Pegzilarginase reduced arginine levels by 80%, normalized arginine levels in 90.5% of patients

Positive trend in mobility measure

31 patients enrolled in long-term extension study First Clinical Program Ever Conducted in ARG1-D 2022 Aeglea BioTherapeutics. External

Double-blind portion of trial complete - topline data announced December 2021 9 PEACE Phase 3 Study Design *Dosing is weekly and, if needed, dose is modified based on plasma arginine levels with maintenance of blinding.

The first 8 weeks of the open-label extension will be blinded. All study participants remain on current disease management for the duration of the trial. Dose adjustments in the double-blind treatment period can be made to optimize plasma arginine control for levels outside the range of 50-150 M. If needed, weekly doses can be increased to 0.15 and 0.2 mg/kg or reduced to 0.05mg/kg

ARG1-D = Arginase 1 Deficiency; IV = intravenous; R = randomized. Patients with ARG1-D

Plasma arginine >250 M (mean)

Baseline deficit in clinical response assessments Placebo IV R 2:1 Long Term Extension Pegzilarginase

0.1 mg/kg* IV 24 weeks Up to 150 weeks n=11 N=32 n=21 N=31 2022 Aeglea BioTherapeutics. External

10 Pegzilarginase Safety Profile - Results from PEACE * TEAE: Treatment-Emergent Adverse Event; SAE: Serious Adverse Event; Adverse Event of Interest

Pegzilarginase was Well-tolerated with No Discontinuations in Pivotal Study Due to Adverse Events No discontinuations due to TEAEs

Most TEAEs were mild or moderate in severity

Common TEAEs occurring in >15% of patients in treatment and placebo arms included vomiting, ammonia increased, cough, hyperammonemia, nausea, abdominal pain, pyrexia, decreased appetite

With exception of vomiting, cough, and pyrexia, each event occurred at lower rate compared to placebo

Hypersensitivity reactions were infrequent (<10% of patients) and managed with routine medical care

SAEs included hyperammonemia and vomiting (1 patient) 2022 Aeglea BioTherapeutics. External

Highly elevated plasma arginine despite standard of care

Mean plasma arginine*

Primary Endpoint - 24-Week Analysis

80% reduction in mean plasma arginine with pegzilarginase (p<0.0001) Primary Endpoint Met - Marked and Sustained Reduction in Plasma Arginine Reduction in Plasma Arginine* *Based on arithmetic mean of values from visit and preceding 3 visits, boxes represent middle 50% with error bars depicting 95% confidence interval; Statistical analysis based on geometric mean` Clinical Guideline 2022 Aeglea BioTherapeutics. External

90.5% of pegzilarginase treated patients achieved normal plasma arginine levels (p<0.0001)*

No meaningful change in plasma arginine levels in placebo arm

Treatment with pegzilarginase surpassed current clinical guideline goals of reducing arginine levels below 200 M 12 Normalization of Plasma Arginine Levels in ARG1-D Patients Proportion of Patients Reaching Normal Arginine Levels (40-115 M) Potential Transformative Therapy for a Patient Population with Previously Unachievable Control of Arginine to Normal Levels * Nominal p value, based on arithmetic mean of values from visit and preceding 3 visits 2022 Aeglea BioTherapeutics. External

PEACE Mobility Assessed by GMFM-E and 2MWT 13 Mean Change from Baseline in 2MWT Mean Change from Baseline in GMFM-E 1 MCID is minimal clinically important difference defined in Cerebral Palsy population. 2Oeffinger D et al 2008; GMFM-E = Gross Motor Function Measure Part E; 2MWT = 2-minute walk test; GMFCS = Gross Motor Function Classification System 2022 Aeglea BioTherapeutics. External

14 Improvements in Mobility Measures Sustained Over Time in Phase 1/2 and OLE 48 1 MCID is minimal clinically important difference defined in Cerebral Palsy population. 2Oeffinger D et al 2008; 3 Analysis weeks are calculated by adding the 8 weeks from Part 2 of the Phase 1/2 study to the weeks of treatment in the open-label extension (OLE) study (e.g., 8 weeks of Part 2 + 12 weeks of OLE is the 20-week analysis); 4 13 patients remain in the OLE study, 9 of 13 patients had 96-week mobility assessments conducted; GMFM-E = Gross Motor Function Measure Part E; 6MWT = 6-minute walk test; SAD = single ascending dose Mean Change from Baseline in GMFM-E Mean Change from Baseline in 6MWT Mean Change (Units) Mean Change (Meters) 2022 Aeglea BioTherapeutics. External

15 Clinically Meaningful Results

Normalized arginine levels which was previously unachievable in this patient population

GMFM-E trend highly suggestive of mobility benefit with improvement over time

Mean changes in both trials greater than MCID of 4 units and 2.8 units for GMFCS Levels I and II respectively1

Strength and consistency of data demonstrate favorable benefit/risk profile

Timeline to Potential U.S. Approval and Launch

Expected BLA submission in first half of 2022

Plan to request priority review

PDUFA date typically ~8 months from submission with priority review

Preparing for strong, rapid launch Confidence in Path to Regulatory Submission and Approvability Robust Regulatory Package Strong Clinical Data Established Manufacturing Multiple Regulatory Designations 1 Oeffinger D et al 2008; MCID = minimal clinically important difference; GMFCS = Gross Motor Function Classification System 2022 Aeglea BioTherapeutics. External

Regulatory Next Steps for BLA Submission Pre-BLA meeting

Discussion of data package and additional submission details