The aim of this study was to compare the effects of plyometric and jump training on physical performance in young male handball players. Twenty-six young male handball players were divided into two sub-groups to perform a five-week pre-season training programme supplemented with two ground-reactive protocols with an equal number of jumping exercises referred as to ground contacts: plyometric training (PLY; n = 14) and standard jump training (CON; n = 12). Before and after training, repeated sprint ability (RSA), jumping ability (JA), maximal oxygen uptake (VO2max) and aerobic power at the anaerobic threshold (PAT) were measured. A two-factor analysis revealed significant time effects with improvements in fat mass (p = 0.012), maximal power during the incremental cycling test (p = 0.001) and PAT (p < 0.001), power decline (PDEC) and maximal power (Pmax) in the 5th repetition (p < 0.05 and p < 0.01, respectively). The training-induced changes in absolute and relative peak power in the RSA test and absolute VO2max approached significance (p = 0.06, p = 0.053 and p = 0.06). No intervention time × exercise protocol effects were observed for any indices of JA, RSA and aerobic capacity. A five-week pre-season conditioning programme supplemented with only 15 sessions of plyometric exercise did not induce any additional benefits, compared to a matched format of standard jump training, in terms of improving jumping performance and maximal power in the RSA test. Aerobic capacity and the fatigue index in RSA were maintained under these two training conditions.