The present study was designed to detect DNA repair response through the homologous recombination pathway in mouse spermatogonial stem cells. Mouse spermatogonial stem cells (mSSCs) were obtained from the adult DBA/2 mouse testes by MACS sorting. mSSCs and mice animals were divided into four groups (30 min, 2, 24 h, control) and treated with ionizing irradiation while the control group received pseudo-irradiation. Proteins involved in the homologous recombination pathway (γH2AX, ATM, RAD51, CtIP, and RPA2) were assessed in mSSCs both in vitro and in vivo. Moreover, the non-homologous end-joining or homologous recombination (NHEJ/HR) reporter plasmids were transfected into mSSCs to assess NHEJ/HR pathway activity after DNA double-strand break (DSB). γH2AX, a classical DNA DSB marker, was absent in mSSCs both in vivo and in vitro after DSB repair, but was highly expressed in other tissue stem cells. In addition, ATM and phosphorylated ATM (p-ATM) were involved in DNA damage response (DDR) in mSSCs. p-ATM foci were overexpressed immediately after irradiation (30 min and 2 h), but gradually decreased over the repair time. The HR pathway-related proteins, CtIP and RPA2 were negatively regulated after treatment in Western blot (WB). NHEJ/HR reporter plasmid transfection indicated that the HR pathway played a minor role in mSSCs during DDR, consistent with the WB findings. This study demonstrates that mSSCs may have a unique response to DNA damage since crucial proteins involved in HR pathway were negatively regulated after DSB. In addition, the expression level of p-ATM, but not γH2AX, was increased after DSB, suggesting that DNA damage repair in mSSCs might be a γH2AX-independent response. Furthermore, the HR pathway may play a minor role during DDR in mSSCs.