Most barnacles are hermaphroditic, although a few species are gonochoric or androdioecious. The ovaries are located in the base or stalk, and may extend into the mantle, while the testes are towards the back of the head, often extending into the thorax. Typically, recently molted hermaphroditic individuals are receptive as females. Self-fertilization, although theoretically possible, has been experimentally shown to be rare in barnacles.

The sessile lifestyle of barnacles makes sexual reproduction difficult, as the organisms cannot leave their shells to mate. To facilitate genetic transfer between isolated individuals, barnacles have extraordinarily long penises. Barnacles have the largest penis to body size ratio of the animal kingdom.