The aim of this study was to compare the effects of functional training (FT) and traditional training (TT) on the physical performance of junior tennis players, as well as to explore how to optimize the training regimen to enhance the effects. We recruited 30 junior tennis players, who were randomly divided into FT and TT groups, and performed different training programs over an 8-week period. The FT group focused on core strength, agility, and balance training, while the TT group used traditional resistance and endurance training. In the fitness test, we focused on a number of metrics such as explosive power (jumping height), agility (T-test time), muscular endurance (60-second-deep squats), specialized speed (20-meter sprint time), and core stability (plank support duration). The results showed that the FT group showed more significant improvements in agility (6.7% shorter T-test time, p<0.05), specialized speed (7.0% shorter 20-m sprint time, p<0.05), and core stability (30.1% longer flatbed support time, p<0.01), while the TT group showed more significant improvements in muscular endurance (18.1% increase in 60-second squats, p<0.05) and explosive power (9.5% increase in jump height, p<0.05). In contrast, there was no significant difference between the two groups in terms of aerobic endurance gains (p>0.05). Overall, functional training is more useful for improving agility and core stability, while traditional training is more suitable for enhancing muscular endurance and explosive power. Based on this, it is recommended to combine the two in the physical training of junior tennis players to give full play to their respective advantages and achieve comprehensive and balanced physical development.