Many species of bats undergo annual migrations, in some cases covering distances of 1,000 km or more. However, very little is known about the physiological and biochemical mechanisms underlying bat migration. In contrast, the physiology of migrating birds has been studied for decades and many migration-related changes have been documented. Although bats and birds evolved flight and long-distance migration independently, they have likely experienced many similar selective pressures. We therefore suggest that knowledge of bird migration physiology can be used to generate predictions for emerging studies of bat migration physiology. In this review, we discuss major physiological and biochemical adaptations relating to fuel acquisition and fuel utilization. For each, we summarize knowledge gained from migration studies of birds and bats (if any) and make predictions of bat migration physiology. For many aspects, we predict that bats will have evolved similar physiological mechanisms to birds. However, there are some potentially major differences in the energetic models for bats and birds, including torpor, fuel selection at high-intensity exercise, and trade-offs between reproduction and migration.