This paper explores ethical issues raised by the application of non-surgical, pharmaceutical fertility control to manage reproductive behaviors in domesticated and wild animal species. We focus on methods that interfere with the effects of GnRH, making animals infertile and significantly suppressing sexual behavior in both sexes. The paper is anchored by considering ethical issues raised by four diverse cases: the use of pharmaceutical fertility control in (a) male slaughter pigs, (b) domesticated stallions and mares, (c) male companion dogs and (d) female white-tailed deer. Ethical concerns explored include animals’ welfare, the possible violation of animals’ rights, including rights to life, reproduction and bodily integrity; and potential concerns about loss of wildness. We compare ethical concerns about pharmaceutical fertility control with alternative strategies for managing animals’ reproductive behavior including (where appropriate) spaying and neutering, sex separation, sex sorting, culling, and doing nothing. The paper concludes that there are some cases where pharmaceutical fertility control is the best ethical choice in current circumstances; but that there are other cases where alternative choices, including doing nothing, would be ethically preferable. This suggests that in ethical terms a case-by-case approach should be taken to the use of pharmaceutical fertility control in animals.