As a defense mechanism against transposable elements, the PIWI‐interacting RNA (piRNA) pathway maintains genomic integrity and ensures proper gametogenesis in gonads. Numerous factors are orchestrated to ensure normal operation of the piRNA pathway. Spindle‐E (Spn‐E) gene was one of the first genes shown to participate in the piRNA pathway. In this study, we performed functional analysis of Spn‐E in the model lepidopteran insect, Bombyx mori. Unlike the germline‐specific expression pattern observed in Drosophila and mouse, BmSpn‐E was ubiquitously expressed in all tissues tested, and it was highly expressed in gonads. Immunofluorescent staining showed that BmSpn‐E was localized in both germ cells and somatic cells in ovary and was expressed in spermatocytes in testis. We used a binary transgenic CRISPR/Cas9 system to construct BmSpn‐E mutants. Loss of BmSpn‐E expression caused derepression of transposons in gonads. We also found that mutant gonads were much smaller than wild‐type gonads and that the number of germ cells was considerably lower in mutant gonads. Quantitative real‐time PCR analysis and TUNEL staining revealed that apoptosis was greatly enhanced in mutant gonads. Further, we found that the BmSpn‐E mutation impacted gonadal development and gametogenesis at the early larval stage. In summary, our data provided the first evidence that BmSpn‐E plays vital roles in gonadal development and gametogenesis in B. mori.