Although many studies have shown that amino acid ingestion acutely stimulates protein anabolism, only few studies have investigated whether long-term supplementation promotes changes in body composition. We therefore tested the hypothesis that l-leucine (LEU) and l-phenylalanine (PHE) supplementation might have a positive impact on the body composition of rats submitted to intermittent periods of food restriction and refeeding (weight cycling or WC). The WC protocol comprised three cycles, each consisting of 1 week of 50% food restriction followed by 2 weeks of ad libitum ingestion. The groups submitted to WC ingested the control diet (WC-CON) or the diet supplemented with LEU+PHE (WC-AA). A pair-fed group receiving the control diet (PF-CON) was used as a reference for the effects of WC. Although food intake was the same in all groups, higher body weight and energy efficiency were observed in the WC-AA group compared to the PF-CON and WC-CON groups although not significantly in relation to the latter. These results were the consequence of a significant increase of lean body mass and body protein content in the WC-AA group compared to the PF-CON and WC-CON groups. The WC-CON and WC-AA groups presented 36.1% and 18.9% more body fat, respectively, than the PF-CON group but this difference was not significant. Neither fasting insulin nor glucose concentration nor postprandial insulin secretion was significantly affected by the supplemented diet. In conclusion, supplementation with LEU+PHE improved the body composition profile of rats submitted to WC, mainly by increasing lean body mass and body protein content.