This study evaluated the effects of feeding time and frequency on growth, morphology, and amino acid composition in juvenile African catfish (Clarias gariepinus) under controlled conditions. A total of 130 fish (6.03 ± 0.16 g) were assigned to four feeding regimes: a control group (A) fed three times daily (08:00, 13:00, 20:00 h) and three groups fed twice daily at different intervals (Group B received feed at 08:00 and 13:00 (morning and afternoon), Group C at 13:00 and 20:00 (afternoon and evening), and Group D at 08:00 and 20:00 (morning and evening). Over eight weeks, data on growth, feed efficiency, carcass traits, organ indices (HSI, VSI, ISI), and amino acid profiles were collected. Feeding schedule significantly affected final weight, feed efficiency, and amino acid retention (p < 0.05). Group D (twice daily, wide interval) matched the control’s growth and nutrient use by Week 5, while Groups B and C showed lower growth and amino acid content, with Group B performing worst. These groups also had reduced BMI, daily growth rate, lipid gain, and organ indices. Whole-body crude protein decreased, and nitrogen-free extract increased in Groups B and C, while Group D remained similar to the control. Muscle protein and essential amino acids (threonine, lysine, methionine, phenylalanine) were significantly lower in Groups B and C but maintained in D. Non-essential amino acids (serine, glycine) followed a similar trend. Overall, synchronizing feeding with the natural rhythms of C. gariepinus enhances growth, nutrient utilization, and health, supporting more efficient aquaculture production.