Purpose: To examine the effects of balance exercises conducted prior to complex training (bCT) versus complex training (CT) only on measures of physical fitness in young female elite handball players. Methods: Participants aged 17 years were randomly assigned to bCT (n = 11) or CT (n = 12). The 2 training interventions lasted 8 weeks with 2 sessions per week in replacement of some technical/tactical handball exercises and were matched for total training volume. Before and after training, tests were performed for the evaluation of proxies of muscle power (countermovement jump height, standing long-jump distance, and reactive strength index), muscle strength (back half-squat 1-repetition maximum), dynamic balance (Y-balance test), linear sprint speed (20-m sprint test), and change-of-direction speed (T test). Results: Two-factor repeated-measures analysis of variance revealed significant group × time interactions for the reactive strength index (d = 0.99, P = .03) and Y-balance test score (d = 1.32, P < .01). Post hoc analysis indicated significant pre–post reactive strength index improvements in CT (d = 0.69, P = .04) only. For the Y-balance test, significant pre–post increases were found in bCT (d = 0.71, P = .04) with no significant changes in CT (d = 0.61, P = .07). In addition, significant main effects of time were observed for half-squat 1-repetition maximum, countermovement jump, standing long jump, and T test performance (d = 1.50 to 3.10, P < .05). Conclusions: Both bCT and CT interventions were effective in improving specific measures of physical fitness in young elite female handball players. If the training goal is to improve balance in addition, balance exercises can be conducted within a CT training session and prior to CT exercises.