Energy intake during the northward migration of tagged juvenile skipjack tuna (Katsuwonus pelamis) was estimated using the heat increment of feeding (HIF) determined through peritoneal cavity temperature data acquired with an archival tag. The effectiveness of this method was confirmed by feeding experiments, even in a species without visceral heat exchangers. Applying these experimental results to the data from tagged fish in the wild revealed that the estimated energy intake of skipjack tuna was, on average, 2.2 times greater in temperate waters than in subtropical waters. This difference was likely due to the differences in the food supply between habitats. In contrast, the estimated energy cost of their daily travel distance decreased with northward migration. This result suggests that skipjack spend less energy in acquiring prey in temperate than in subtropical waters since prey are available in higher densities, thereby providing excess energy for growth or lipid reserves.