The present study was designed to investigate and compare the effects of game profile-based (GPBT) and small-sided games (SSGs) training on physical performances of elite youth soccer players during the in-season period. Twenty young soccer players (18.6 ± 0.6) were randomly assigned to either GPBT or SSGs protocols performed twice a week for 8 weeks. The GPBT consisted of 2 sets of 6-10 min of intermittent soccer specific circuits. The SSGs training consisted of 3-5 sets of 5 vs. 5 SSGs played on a 42 x 30 m pitch. Before and after the training program, the following physical performance were assessed: repeated sprint ability (RSA), change of direction (COD), linear sprinting on 10-m and 20-m, jumping (CMJ), and intermittent running (YYIRL1). Significant improvements were found in all the assessed variables following both training interventions (p < 0.05). The GPBT group improved more than the SSGs group in the 10-m and 20-m sprint tests by 2.4% (g = 0.4; small effect) and 4% (g = 0.9; large effect), respectively. Conversely, the SSGs group jumped 4% higher (g = 0.4; small effect) and resulted 6.7% quicker than the GPBT (g = 1.5; large effect) in completing the COD task. These results suggest both GPBT and SSGs to be effective for fitness development among elite young soccer players during the competitive season. More importantly, these two conditioning methodologies may be considered in terms of specificity for selectively improving or maintaining specific soccer fitness-related performances in the latter phase of the season.