A plethora of semi‐aquatic species perform seasonal migrations to reproduce, with migration timing often relating to several factors. Human‐induced environmental changes may disrupt the migration phenology of many taxa. Improving our knowledge on drivers of migration phenology helps to elucidate the impacts of climate change upon biodiversity. Herein, we applied circular analyses to investigate how biological and environmental factors affect the migration phenology of leaf litter frogs in an Atlantic forest remnant. We observed the synchronous arrival at ponds of adults Physalaemus, likely due to its short breeding period and opportunistic breeding strategy. Large‐sized females arrived earlier than small‐sized ones at the ponds likely due to their higher movement potential. Temperature, precipitation and photoperiod affected the immigration phenology of females, but not of males. Only photoperiod affected emigration phenology of male Physalaemus. The higher responsiveness of females to environmental cues suggests they migrate when environmental conditions are optimal. Lastly, the emigration phenology of juvenile Physalaemus occurred in ‘bursts’, with precipitation likely triggering departure from ponds. Overall, we showed that sex‐related differences in responses to environmental cues could exacerbate phenological shifts in amphibian migrations due to environmental changes, and potentially impact the mating success of forest‐dependent pond‐breeding species.