There is an ongoing discussion about how to improve jump performance most efficiently with plyometric training. It has been proposed that drop height influences the outcome, although longitudinal studies are missing. Based on cross-sectional drop jump studies showing height-dependent Hoffmann (H)-reflex activities, we hypothesized that the drop height should influence the neuromuscular activity and thus, the training result. Thirty-three subjects participated as a control or in one of two stretch-shortening cycle (SSC) interventions. Subjects either trained for 4 weeks doing drop jumps from 30, 50, and 75 cm drop heights (SSC1) or completed the same amount of jumps exclusively from 30 cm (SSC2). During training and testing (from 30, 50, and 75 cm), subjects were instructed to minimize the duration of ground contact and to maximize their rebound height. Rebound heights were significantly augmented after SSC1, but a trend was only observed after SSC2. In contrast, the duration of ground contact increased after SSC1 but decreased after SSC2. The performance index (rebound height/duration of ground contact) improved similarly after SSC1 (+14%) and SSC2 (+14%). Changes in performance were accompanied by neuromuscular adaptations: for SSC1, activity of the soleus increased toward take-off (between 120 and 170 ms after touchdown), whereas SSC2-trained subjects showed enhanced activity shortly after ground contact (20–70 ms after touch down). The present study demonstrates a strong link among drop height, neuromuscular adaptation, and performance in SSC training. As the improvement in the performance index was no different after SSC1 or SSC2, the decision whether to apply SSC1 or SSC2 should depend on the specific requirements of the sports discipline.