Between late austral autumn and early winter, some of the Magellanic penguin Spheniscus magellanicus population foraging on the Patagonian continental shelf move towards the southern Brazilian coast (22–32°S). Many of these vagrant birds wash ashore in very poor health condition. The Santos Municipal Aquarium, Brazil, takes in some of those stranded individuals and provides a programme of rehabilitation. The surviving birds are retained for public exhibition and environmental education. This study describes the husbandry practices and veterinary care for the penguins developed at the Aquarium, including data on survivorship, sex, ontogeny, death rates, reproduction and time in captivity. Most of the received penguins were found in Santos (23·9°S), but there were animals collected between Bertioga and Cananéia (23·7–25·3°S). The highest incidence of stranded animals was recorded in 2008. Most animals were collected during austral winter and no penguins were received in March and April. Most animals were juvenile on arrival at the institution. The average time rehabilitated birds remained in captivity (i.e. the quarantine period plus time on public exhibition) was 294 days, with a longest time of 3681 days. The most common diseases recorded in captivity were bumblefoot and aspergillosis, whereas helminth parasite infestations were the commonest ailment recorded in newly rescued birds. One individual hatched at the Aquarium in 2001 and two others in 2017.