Small RNAs can silence transposons at transcriptional or post-transcriptional level. Newly identified small RNAs (e.g., piRNAs and endo-siRNAs) can repress the activity of transposons. Drosophila piRNAs, mouse piRNAs, mouse endo-siRNAs, and their related proteins are expressed primarily within the germline. This suggests that the small RNA pathway plays an important role in transposon silencing of the germline. Recent studies revealed the connection between small RNAs, transposon silencing, and the regulation of fertility, but the mechanism has not been clarified in detail. In this review, the advances in the control of genomic transposon activity and the regulation of fertility by the small RNA pathway were summarized and discussed.