The aim of the present study was to evaluate two different intervention programs applied during a 4-week pre-season period. Twenty-nine players participated in this study and were divided into two groups. One group (BallTrain, n = 12, age: 17.8 ± 0.4 years, body mass: 73.9 ± 7.6 kg, height: 178 ± 0.1 cm, body fat: 9.6 ± 5.3%) performed a higher percentage of aerobic training with ball and strength training using plyometrics and exercises with body weight. The other group (HIITTrain, n = 17, age: 17.8 ± 0.7 years, body mass: 73.3 ± 5.0 kg, height: 179 ± 0.1 cm, body fat: 8.0 ± 2.3%) trained with high-intensity interval training (HIIT) without the ball and performed resistance training with weights in the same session. Both groups trained for strength (two times/week) and performed aerobic–anaerobic fitness without the ball, passing games, and tactical and small-sided games. Lower limb power (CMJ) and aerobic fitness (Yo-Yo intermittent recovery test level 1-IR1) were evaluated before and after the four-week training program. Yo-Yo IR1 performance was improved in both groups, but the improvement was greater for the HIITTrain than BallTrain group (468 ± 180 vs. 183 ± 177 m, p = 0.07). CMJ showed a non-significant improvement in the BallTrain group (5.8 ± 8.8%, p = 0.16), but it decreased by 8.1 ± 9% (p = 0.001), in the HIITTrain group. In conclusion, we have shown that a short pre-season period of training results in improvements in aerobic fitness in both groups, with high-intensity interval training showing superior adaptations than training with the ball. However, CMJ performance was reduced in this group, possibly suggesting higher fatigue levels and overload, and/or showing the effects of concurrent HIITTrain and strength training in soccer.