Exhibit 99.1

Magenta Therapeutics Reports Third Quarter Financial Results

and Recent Program Highlights

– New clinical results from ongoing MGTA-117 Phase 1/2 clinical trial support earlier observations of target binding, target cell depletion, rapid drug clearance and a favorable tolerability profile; clinical trial has progressed into the third dose escalation cohort; oral presentation of clinical data will be given at the 2022 American Society of Hematology (ASH) meeting in December 2022 –

– CD45 antibody-drug conjugate (ADC) dose-ranging toxicology study successfully completed; IND-enabling studies advancing; program update and development timeline guidance anticipated in December 2022 –

– MGTA-145 stem cell mobilization clinical trial in sickle cell disease patients is enrolling with early clinical data expected in December 2022 –

– Approximately $128.3 million in cash, cash equivalents and marketable securities at the end of Q3 2022; maintains guidance that cash reserves are expected to fund current operating plan into Q2 2024 –

Cambridge, MA – November 3, 2022 – Magenta Therapeutics (Nasdaq: MGTA), a clinical-stage biotechnology company developing novel medicines designed to bring the curative power of stem cell transplant to more patients, today reported financial results for the third quarter ending September 30, 2022, and recent program highlights.

“We are building momentum in the MGTA-117 clinical trial with new clinical results and are making progress across our pipeline, including our second targeted conditioning program CD45-ADC,” said Jason Gardner, President and Chief Executive Officer of Magenta Therapeutics, Inc. “In the MGTA-117 Phase 1/2 clinical trial, we continue to enroll and generate clinical data in higher-dose cohorts. Our preclinical work has been particularly helpful in predicting our clinical experience in these early dose cohorts regarding MGTA-117 activity at different exposure levels and the overall tolerability profile. We look forward to presenting available clinical data at ASH and using our data to support interactions with regulators as we plan to advance MGTA-117 to stem cell transplant-eligible patients and into gene therapy.”

Program Highlights:

MGTA-117 Phase 1/2 Clinical Trial Progression and Data Disclosure Expectations

MGTA-117 is Magenta’s most advanced targeted conditioning product candidate designed to deplete target cells prior to a patient undergoing stem cell transplant or receiving an ex vivo gene therapy product. The program is currently enrolling patients with relapsed/refractory acute myeloid leukemia (AML), and myelodysplastic syndromes (MDS), in a Phase 1/2 dose escalation clinical trial. MGTA-117 is an anti-CD117 antibody conjugated to an amanitin payload. CD117, also known as c-Kit receptor, is highly expressed on hematopoietic stem cells, progenitor cells, and leukemic cells.

CD45-Antibody Drug Conjugate (ADC): Second Targeted Conditioning Program

Magenta’s CD45-ADC is designed to selectively target and deplete both stem cells and immune cells and is intended to replace the use of chemotherapy and radiation-based conditioning prior to stem cell transplant in patients with blood cancers and autoimmune diseases.

MGTA-145 Stem Cell Mobilization and Collection

Magenta is developing MGTA-145, in combination with plerixafor, to improve the process by which stem cells are released out of the bone marrow and into the bloodstream, known as stem cell mobilization. The mobilized cells are then collected and available for transplant. This is the first step for patients and is required for the majority of transplants and stem cell gene therapies.

Financial Results:

Cash Position: Cash, cash equivalents and marketable securities as of September 30, 2022, were $128.3 million, compared to $176.9 million as of December 31, 2021. The September cash balance includes gross proceeds of $3.0 million from our “at-the-market” facility. Magenta anticipates that its cash, cash equivalents and marketable securities will be sufficient to fund its current operational plan into Q2 2024.

Research and Development Expenses: Research and development expenses were $11.2 million in the third quarter of 2022, compared to $10.8 million in the third quarter of 2021. The increase was driven primarily by higher preclinical and manufacturing costs to support our IND-enabling studies for CD45-ADC, offset by a decrease in clinical trial costs related to our mobilization program.

General and Administrative Expenses: General and administrative expenses were $6.1 million for the third quarter of 2022, compared with $7.5 million in the third quarter of 2021. The decrease was primarily due to a decrease in stock-based compensation.

Net Loss: Net loss was $16.1 million for the third quarter of 2022, compared to net loss of $17.4 million for the third quarter of 2021.

About Magenta Therapeutics

Magenta Therapeutics is a clinical-stage biotechnology company developing medicines designed to bring the curative power of stem cell transplant to more patients with blood cancers, genetic diseases and autoimmune diseases. Magenta is combining leadership in stem cell biology and biotherapeutics development with clinical and regulatory expertise to revolutionize blood and immune reset to allow more patients to take advantage of the curative potential of stem cell transplant and potentially improve eligibility for future gene therapies.

Magenta is based in Cambridge, Mass. For more information, please visit www.magentatx.com.

Follow Magenta on Twitter: @magentatx.

Forward-Looking Statements

This press release contains forward-looking statements within the meaning of The Private Securities Litigation Reform Act of 1995, as amended. These statements include, without limitation, implied and express statements relating to: Magenta’s future business expectations, plans and prospects; the potential of, and expectations for, Magenta’s product candidate pipeline; the potential benefits and expected performance of Magenta’s product candidates and programs; the development of product candidates and advancement of preclinical and clinical programs, including, without limitation, patient enrollment; expectations, plans and timing for preclinical activities, clinical trials and related results involving Magenta’s product candidates; expectations, plans and timing for the generation, receipt and disclosure of preclinical and clinical trial data, toxicology results, and other results involving Magenta’s product candidates; timing for the disclosure of developmental timelines, developmental plans and program updates regarding Magenta’s product candidates; timelines and expectations for dosing, dosing regimens and administration; the use of data to support interactions with regulators as Magenta plans to advance MGTA-117 to stem cell transplant-eligible patients and into gene therapy; the

completion of dose-limiting toxicity observation periods; regulatory interactions; the planned transition of the MGTA-117 Phase 1/2 clinical trial into transplant-eligible AML and MDS patients; expectations that regulatory interactions will focus on MGTA-117’s clinical data relating to target binding, drug clearance and stability and tolerability across multiple dose levels; the planned use of available clinical data to support regulatory interactions, as well as the predictive preclinical modeling in non-human primates that has closely matched Magenta’s clinical experience; expectations that data from the Phase 1/2 trial will inform clinical development planning and enable regulatory engagements for MGTA-117 as a potential monotherapy prior to patients undergoing autologous ex vivo gene therapy; the predictive value of Magenta’s MGTA-117 preclinical modeling; whether present results will collectively inform the continued development of MGTA-117; the anticipation of entering into additional collaborations as data progresses; that data from a dose-ranging toxicology preclinical study for CD45-ADC inform dosing for a Good Laboratory Practices toxicology study intended to support a planned Investigational New Drug application; the expectation that clinical data from additional dose-escalation cohorts will support Magenta’s prior clinical observations and data in the MGTA-117 Phase 1/2 clinical trial in patients with relapsed/refractory AML and MDS; the anticipated benefits of Magenta’s revised operating plan; and Magenta’s current anticipation and guidance regarding the ability of its cash, cash equivalents and marketable securities to fund its current operating plan into Q2 2024.

Words such as “anticipate,” “believe,” “continue,” “could,” “designed,” “endeavor,” “estimate,” “expect,” “intend,” “may,” “might,” “plan,” “potential,” “predict,” “project,” “seek,” “should,” “target,” “preliminary,” “will,” “would” and similar expressions are intended to identify forward-looking statements. The express or implied forward-looking statements included in this press release are only predictions and are subject to a number of risks, uncertainties and assumptions, including, without limitation: volatility and uncertainty in the capital markets for biotechnology companies; uncertainties inherent in preclinical and clinical trials and in the availability and timing of data from ongoing and planned clinical and preclinical trials; the ability to initiate, enroll, conduct or complete ongoing and planned preclinical and clinical trials; vulnerability and/or fragility of, and the presence of underlying disorders in, the patient population for the clinical trials of Magenta’s product candidates, including the MGTA-117 Phase 1/2 clinical trial in patients with relapsed/refractory AML and MDS; the delay of any current or planned preclinical or clinical trials, or the delay in development of Magenta’s product candidates; whether results from preclinical or earlier clinical trials will be predictive of the results of future trials; interactions with regulatory agencies such as the U.S. Food and Drug Administration; the expected timing of submissions for regulatory approval to conduct or continue trials or to market products; Magenta’s ability to successfully demonstrate the safety and efficacy of its product candidates; whether Magenta’s cash

resources will be sufficient to fund Magenta’s foreseeable and unforeseeable operating expenses and capital expenditure requirements; and risks, uncertainties and assumptions regarding the impact of the continuing COVID-19 pandemic on Magenta’s business, operations, preclinical activities, clinical trials, strategy, goals and anticipated timelines. These and other risks are described in additional detail in Magenta’s Quarterly Report on Form 10-Q for the quarter ended September 30, 2022, expected to be filed on or about November 3, 2022, and its other filings made with the Securities and Exchange Commission from time to time. Any forward-looking statements contained in this press release represent Magenta’s views only as of today and should not be relied upon as representing its views as of any subsequent date. Magenta explicitly disclaims any obligation to update any forward-looking statements, except to the extent required by law.

Contact:

Jill Bertotti, Real Chemistry (advisor to Magenta)

714-225-6726

jbertotti@realchemistry.com

Magenta Therapeutics, Inc.

STATEMENTS OF OPERATIONS

(unaudited)

(In thousands, except share and per share data)

BALANCE SHEET DATA

(unaudited)

(In thousands)