The peak velocity of an athlete’s throws is a determining factor for sports performance. The aim of this study was to analyze the effects of a post-activation performance enhancement (PAPE) protocol with functional electro-mechanical dynamometry (FEMD) on throwing velocity. Thirteen international-level female handball players voluntarily participated in the study. The PAPE protocol considered four sets of eight repetitions controlled by FEMD (four at 30% of 1RM followed by another four at 60% of 1RM). After each series, the athletes’ throwing velocity was measured. Significant differences (p < 0.01) were found in the effect size (ES), which measures the strength of the statistical relationship between two variables by group with the repeated measures ANOVA statistic with an effect size ω2 = 0.028. The effect size analysis identified measurements that are considered null for the baseline—PAPE 1 comparison and small baseline—PAPE 2, baseline—PAPE 3, and baseline—PAPE 4. When resistance is controlled during the run as with an FEMD device, only two sets of eight repetitions (four repetitions at 30% and four repetitions at 60% of 1RM) are required for the improvement of throwing speed in elite handball players.