Several studies have recently revealed the regulatory mechanisms underlying female germline stem cell (FGSC) differentiation, proliferation, and apoptosis, but other biological processes such as autophagy and its mechanism in FGSCs are largely unclear. The use of small chemical compounds may be a good approach to further investigate the process and mechanism of autophagy in FGSC development. In this study, we used ZCL-082, a derivative of benzoxaboroles, to treat FGSCs. Using a cell counting kit-8 (CCK8) and 5-ethynyl-2′-deoxyuridine (EdU) assays, we found that ZCL-082 could significantly reduce the viability, proliferation, and number of FGSCs
in vitro
. Moreover, western blotting revealed that the expression of light chain 3 beta 2 (LC3B-II) in FGSCs was significantly increased after treatment with ZCL-082 for 3 and 6 h. Meanwhile, the expression of sequestosome-1 (SQSTM1) was significantly decreased. These results suggested that ZCL-082 can induce autophagy of FGSCs
in vitro
. Regarding the molecular mechanism, ZCL-082 could significantly reduce the expression of growth arrest-specific 5 (
GAS5
) long non-coding RNA, which could directly bind to microRNA-21a (
miR-21a
) and negatively regulate each other in FGSCs. Knockdown of
GAS5
induced the autophagy of FGSCs, while
GAS5
overexpression inhibited the autophagy of FGSCs
in vitro
and rescued FGSC autophagy induced by ZCL-082. Additionally, overexpression of
miR-21a
significantly enhanced LC3B-II protein expression while significantly reducing the expression of programmed cell death protein 4 (PDCD4) and SQSTM1 protein in FGSCs compared with control cells. The inhibition of
miR-21a
significantly reduced the basal or ZCL-082-induced upregulated expression of LC3B-II, and it significantly enhanced the expression of PDCD4 while downregulating the basal or ZCL-082-induced expression of SQSTM1 in FGSCs. Furthermore, the overexpression of GAS5 enhanced the protein expression of PDCD4, but knockdown of GAS5 reduced the protein expression of PDCD4. Taken together, these results suggested that ZCL-082 induced autophagy through
GAS5
functioning as a competing endogenous RNA (ceRNA) sponge for
miR-21a
in FGSCs. It also suggested that the
GAS5
/
miR-21a
axis may be a potential therapeutic target for premature ovarian failure in the clinic.