Activation of the mechanistic target of rapamycin (mTOR) pathway is known to promote protein synthesis by enhancing mRNA translation. However, there have been few literatures on the effect of mTOR on protein metabolism in non-mammals. The main source of ammonia in fish comes from protein catabolism. The key step of protein catabolism involves the deamination and/or transamination of amino acids. This study is aimed to explore the mechanism underlying mTOR pathway influencing protein retention from the perspective of protein catabolism. Chinese perch were fasted for 24 h and divided into 4 groups randomly before intracerebroventricular (ICV) injection: (1) control group for leucine; (2) leucine group; (3) control group for leucine and rapamycin; (4) leucine and rapamycin group. Food intake was equivalent between each control and treatment groups at each time point (0.5, 4, 12 and 24 h post-injection). Ammonia-N excretion rate, blood glucose, S6 phosphorylation level, and expression of relative genes of protein catabolism (GDH, AMPD, AST, ALT) were determined. The results indicated that the pS6 level was increased, and that the ammonia-N excretion rate, blood glucose, and mRNA level of protein catabolism genes (GDH and AMPD) were significantly decreased after injection with leucine, while those changes were reversed after injection with leucine and rapamycin. Our study not only reveals the mechanism by which mTOR mediates protein synthesis by inhibiting protein catabolism in Chinese perch, but also provides reference for improving the utilization of feed protein.