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This study aimed to compare the post-activation potentiation performance enhancement (PAPE) response to the acute inertial flywheel (FW) and free weight resistance training (TRA) on subsequent countermovement jump (CMJ) and sprint performance (10 m sprint). This study used a randomized crossover design including twenty-eight healthy males that were divided into strong (relative one-repetition maximum (1RM) back squat > 2.0 × body mass) and weak (relative 1RM back squat < 2.0 × body mass) groups. All participants performed the following: (a) three reps at 90% of their 1RM back squat (TRA) and (b) three reps on an inertial FW (plus one repetition to initiate flywheel movement) with an intensity that generated a mean propulsive velocity equal to that achieved with 90% of the 1RM back squat. Before and after the conditioning activity, participants performed two CMJs and two 10 m sprints. Within-group analyses showed significantly greater CMJ (<i>d</i> > 0.9, <i>p</i> < 0.001) and sprint performance (<i>d</i> > 0.5, <i>p</i> < 0.05) in the FW and the TRA group. Between-group analysis showed that sprint changes were significantly greater in the FW-strong group when compared with the TRA (F_1,18 = 5.11, <i>p</i> = 0.036, η²_p = 0.221—large) group. These results suggest that using a squat activation protocol on a FW may lead to an acute positive effect on jump and sprint performance, especially in stronger individuals.