Myeloid-derived suppressor cells (MDSCs) are a group of heterogeneous immature myeloid cells and display immunosuppressive function. In this study, MDSCs populations were evaluated in acquired aplastic anemia (AA) (n=65) in which aberrant immune mechanisms contributed to bone marrow destruction. Our data demonstrate that both the proportion and immunosuppressive function of MDSCs are impaired in AA patients. Decreased percentage of MDSCs, especially monocytic-MDSCs, in the blood of AA patients (n=15) is positively correlated with the frequency of T regulatory cells, bone marrow level of WT1 and decreased plasma level of arginase-1. RNA sequence analyses reveal that multiple pathways including DNA damage, interleukin (IL)-4, apoptosis, and Janus kinase (JAK)-signal transducer and activator of transcription (STAT) are upregulated, whereas transcription, IL-6, IL-18, glycolysis, transforming growth factor and reactive oxygen species are downregulated in MDSCs of AA (n=4), compared with that of healthy donors (n=3). These data suggest that AA MDSCs are defective. Administration of rapamycin significantly increases the absolute number of MDSCs and levels of intracellular enzymes, including arginase-1 and inducible nitric-oxide synthase. Moreover, rapamycin inhibits MDSCs from differentiating into mature myeloid cells. These findings reveal that impaired MDSCs are involved in the immunopathogenesis of AA. Pharmacologically targeting of MDSCs by rapamycin might provide a promising therapeutic strategy for AA.