This study aimed to examine the effects of two different complex training protocols on physical performance in highly-trained youth basketball players. Fourteen adolescent players participated in twice-weekly sessions over eight weeks, following either the Drop Jump protocol (n = 7) or the Tic-tac protocol (n = 7), performing 1–3 sets of 8–9 exercises. Physical performance was assessed before and after the intervention using jumping tests (CMJ, squat, 10–5 hop jumps), change-of-direction speed (5-10-5), sprinting (0–20 meters), and muscular strength (isometric midthigh pull) tests. The intraclass correlation coefficient of within subjects measures was 0.95. Results showed no significant fixed effects for group or time on performance variables (p > 0.05), with greater variance attributed to measurements rather than group differences. The interindividual response to training was highly variable, contingent on the performance outcome. These findings suggest that the parkour-based Tic-tac protocol can be included in strength and conditioning programs for youth basketball players to enhance sport-specific actions. However, to improve physical performance in young team-sport athletes, it is crucial to address the individual needs of each athlete. This includes acknowledging the highly individualised responses to training stimuli.