Acquired aplastic anemia (AA) is a rare hematologic disease characterized by a profound pancytopenia and hypocellular bone marrow. To comprehensively compare the efficacy and safety of allogeneic hematopoietic stem cell transplantation (allo-HSCT) with immunosuppressive therapy (IST) as a front-line treatment for patients with AA. We searched the Medline, Embase, and Cochrane Registry of Controlled Trials databases from January 2000 to March 2019. Studies comparing allo-HSCT with IST as a first-line therapy for patients with AA were included. Fifteen studies including a total of 5336 patients were included in the meta-analysis. The pooled hazard ratio (HR) for overall survival (OS) was 0.4 (95% CI 0.074–0.733, P = 0.016, I2 = 58.8%) and the pooled HR for failure-free survival (FFS) was 1.962 (95% CI 1.43–2.493, P = 0.000, I2 = 0%). The pooled relative risk (RR) for overall response rate (ORR) was 1.691 (95% CI 1.433–1.996, P = 0.000, I2 = 11.6%). Although survival was significantly longer among AA patients undergoing first-line allo-HSCT compared to those undergoing first-line IST, the selection of initial treatment for patients with newly diagnosed AA still requires comprehensive evaluation of donor availability, patient age, expected quality of life, risk of disease relapse or clonal evolution after IST, and potential use of adjunctive eltrombopag.