The Drosophila master sex‐switch protein Sex‐lethal (SXL) regulates the splicing and/or translation of three known targets to mediate somatic sexual differentiation. Genetic studies suggest that additional target(s) of SXL exist, particularly in the female germline. Surprisingly, our detailed molecular characterization of a new potential target of SXL, enhancer of rudimentary (e(r)), reveals that SXL regulates e(r) by a novel mechanism—polyadenylation switching—specifically in the female germline. SXL binds to multiple SXL‐binding sites, which include the GU‐rich poly(A) enhancer, and competes for the binding of CstF64 in vitro. The SXL‐binding sites are able to confer sex‐specific poly(A) switching onto an otherwise nonresponsive polyadenylation signal in vivo. The sex‐specific poly(A) switching of e(r) provides a means for translational regulation in germ cells. We present a model for the SXL‐dependent poly(A) site choice in the female germline.