Background: Although the literature has described different ways and methodologies of producing chronic neuromuscular enhancements in athletes, less is known about warm-up activities aiming to optimize short-term performance. To address these gaps, investigations into post-activation performance enhancement (PAPE) effects are necessary. As such, this work aimed to analyse the PAPE effect of different parallel squat (PS) protocols with and without whole-body vibration (WBV) employing different volumes (low and high) and rest periods (of one and four minutes) on jumping performance. Methods: Seventeen elite sprinting and jumping male athletes participated in this study. The athletes completed one PAPE protocol on a weekly basis, according to the following conditions: PS with 80% one-repetition maximum (1RM) without vibration (NV-PS) and with WBV (WBV-PS). Each exercise was performed at a high and low volume, and after short or long recovery periods (of one and four minutes). A countermovement jump (CMJ) and drop jump (DJ) without an arm swing were executed before and after each PAPE protocol. Results: Higher CMJ and DJ performances after WBV-PS exercises were found (effect size [ES] = 1.065–1.319, large). Greater DJ results were observed after an NV-PS exercise with a high volume and four minutes of rest (37.78 ± 5.44 vs 39.09 ± 5.62; p = 0.011; ES = 0.692, medium). Time x condition effects (F = 25.239, p < 0.01, η^2= 0.03) were observed, revealing higher CMJ values after a WBV-PS in comparison to baseline conditions, as well as higher DJ values after NV-PS and WBV-PS in comparison to baseline conditions. Conclusions: The findings indicate that these types of PAPE protocols in elite male athletes and WBV-PS PAPE protocols in particular can enhance CMJ and DJ performance, while the NV-PS (using a high volume and four minutes of rest) resulted in improvements for the DJ. No other improvements were reported using NV-PS combinations.