Purpose This study aimed to compare the post-activation performance enhancement (PAPE) induced by isometric and isotonic exercise on vertical jump performance. Methods 18 healthy trained men (25.8±2.7 years; 78.4±8.2 kg; 175.7±6.1 cm; 25.4±1.8 BMI; 126.72±10.8 kg squat 1-RM) volunteered for this study. They randomly performed two different PAPE protocols: Isotonic squats (ISOTS), which consisted of 2 sets of 3 repetitions at 75% of one-maximum repetition (1-RM); and isometric squats (ISOMS), which consisted of 2 sets of 4 seconds of submaximal (75% of 1-RM) isometric contraction at 90°-knee flexion. Countermovement jump (CMJ) height was tested at baseline and 4 minutes after each conditioning set. Results CMJ height significantly increased after set 1 in both PAPE protocols (ISOMS: p <0.001; ES = 0.34; ISOTS: p <0.001; ES = 0.24), with respect to the baseline jump. However, after set 2 no significant changes in CMJ height were observed for any protocol (ISOMS: p = 0.162; ES = 0.11; ISOTS: p = 0.976; ES = 0.06). No significant differences (p>0.05) were found between both isometric and isotonic exercise conditions. Conclusions Despite both protocols showed similar PAPE effects on CMJ height after set 1, none of the protocols demonstrated greater efficacy in increasing subsequent performance in healthy trained men.