Pejerrey is a freshwater fish from South America with high potential for aquaculture. This study was designed to determine the effects of different dietary protein:lipid ratio on growth rate and the expression of growth, lipid metabolism and feeding-related genes of this species during early developmental stages. Pejerrey fry were fed for 60 days with four experimental diets containing low (400 g Kg−1) or high (500 g Kg−1) protein (LP or HP, respectively) and low (120 g Kg−1) or high (200 g Kg−1) lipid (LL or HL, respectively), in the combinations: LP-LL; LP-HL; HP-LL and HP-HL. Measurements of growth, lipid and fatty acid content of fry, expression of genes from the endocrine axis (gh, ghrs, igfs), fatty acid metabolism (∆6-desaturase), and food intake behavior (nucb2/nesfatin-1) were collected. Fry fed with diets LP-LL and HP-LL showed the highest growth rate and growth hormone (gh) mRNA expression levels. The gene expression of ∆6-desaturase was high in head of fry fed with diet LP-HL. The mRNA expression of nucb2/nesfatin-1 and gh followed the same patterns in head, and the inverse pattern in body. In conclusion, diets with LL ensure a higher growth of pejerrey fry compared to those that contain HL, without altering the final lipid amount nor the fatty acid profile on fry. In LL groups, the expression of genes from the GH-IGF axis is associated with the observed promotion of somatic growth. The expression of nucb2/nesfatin-1 indicates an effect of this peptide not related to food intake regulation, e.g., a negative regulatory role on GH expression, that would warrant future research.