Fish protein is a source of animal protein that is consumed worldwide. Although it has been reported that the intake of Alaska pollack protein (APP) reduces serum triglyceride and body fat accumulation in rats, the mechanisms underlying these effects are poorly understood. In the present study, we fed 5-week-old male Sprague-Dawley rats a high-fat diet with APP or casein for 4 weeks. We reconfirmed that the intake of APP decreases serum triglycerides and inhibits visceral body fat accumulation in rats. We found that APP had a higher non-digestive protein content than casein, and the amount of protein in feces was higher in the APP group than in the casein group. However, the amount of total lipids in feces did not differ significantly between the groups. We also found that the gastrocnemius muscle, a fast-twitch muscle, tended to increase in weight, and that the epididymal fat weight correlated negatively with gastrocnemius muscle weight in the APP group. These results imply that the enhancement of basal energy expenditure by fast-twitch muscle hypertrophy, rather than the enhancement of lipid excretion via feces, partly causes APP-induced inhibition of lipid accumulation in rats.