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Rugby players must develop excellent levels of conditioning during adolescence. However, this pivotal period of life is also characterized by a surge in biological growth, which further increases the energy and nutritional requirements of this population. This study examined within-individual differences in energy intake (EI) and energy balance (EB) of 46 young rugby players during a pre-season micro-cycle. Two clusters were identified with significantly different characteristics and EB states, suggesting that young rugby players adjust their EI to match their body composition goals. The first cluster is characterized by players with a low body fat% (12.87 ± 2.53). They had a positive EB (330 ± 517 kcal), suggesting a goal of increasing muscle mass. Conversely, the second cluster is characterized by a higher body fat% (23.1 ± 1.6, p < 0.005) and reported a negative, lower EB (-683 ± 425 kcal, p < 0.005), suggesting a goal focused on reducing fat mass. Although our study provides more optimistic results than previous ones regarding the high risk of inadequate EI in young rugby players, we emphasize the importance of rigorous nutritional support, especially for players aiming to lose weight, to avoid severe caloric restriction, as well as the downstream effects of such practices on their nutritional status, given the higher risk of macro- (e.g., CHO < 6 g/kg/d) and micronutrient (e.g., iron < 11 mg/d, calcium < 1300 mg/d, vitamin D < 5 mg/d) deficiencies.