The objective of this study was to investigate the effects of different durations of early carbohydrate (CHO) feeding stimulus on the growth performance and CHO metabolism of Nile tilapia later in life. The first-feeding nutritional stimulus treatments were a low-CHO/high-protein diet for 3 weeks (control group), a short duration high-CHO/low-protein (HC/LP) diet for 1 week (short-HC/LP group), and a long duration HC/LP diet for 3 weeks (long-HC/LP group). As expected, compared to the control fry, the short- and long-HC/LP diets were associated with lower growth performance in the fry at the end of the stimulus period, which was associated with differential gene expression for protein and glucose metabolism, followed by compensatory growth later. Subsequently, to test the existence of CHO metabolic programming, juvenile fish were challenged with a high-CHO diet in weeks 21–24. Our results show that early HC/LP stimulus improved the growth performance of juveniles, suggesting that a history of early HC/LP stimulus contributes to better use of dietary CHO for growth. Interestingly, metabolism modifications linked to early HC/LP stimulus were observed in many of the parameters, irrespective of the duration of early stimulus. The upregulation of the glucose gene (involved in glycolysis and transport) in juveniles that experienced early stimulus and the downregulation of genes involved in gluconeogenesis and amino acid catabolism can explain the improved use of the CHO diet in these fish. Taken together, early HC/LP feeding in tilapia fry is associated with highly significant metabolic programming later in life. Moreover, because the long-HC/LP treatment had stronger direct negative effects on growth performance than the short-HC/LP treatment, this study suggests that a 1-week early HC/LP feeding period could be sufficient to program juvenile tilapia for better nutrient use.