Background: This study analyzed the effects of short-term, off-season physical training on the core dynamic and thigh muscle function of youth soccer players. Methods: For two weeks during the off-season, middle-school soccer players (MSP, n = 75) and high-school soccer players (HSP, n = 104) participated in exercise training (five times per week). Their body composition, physical fitness, core dynamic balance, and isokinetic muscle function were compared before and after training. Results: Both groups showed significant (p 0.01) decreases in body composition, and significant (p 0.01) improvements in physical fitness (MSP, 1.02–1.15%; HSP, 1.05–3.76%). In terms of core dynamic balance, both groups showed a significant (p 0.01) increase in back strength (MSP, 1.09–1.11%; HSP, 1.06–1.16%), and a significant (p 0.05) decrease in the left-right difference (MSP, 0.70–1.43%; HSP, 1.00–1.09%) after training. For isokinetic muscle function at the knee joint, the MSP group showed significant improvement in flexors, whereas the HSP group showed significant improvements in both the extensors and flexors. The dominant vs non-dominant deficit decreased significantly in the MSP group for total work and average power per repetition of the flexors at 60 deg/sec and in the HSP group for peak torque and total work of the flexors at 60 deg/sec. The hamstring-to-quadriceps ratio increased significantly at 60 deg/sec on the dominant side in the MSP group. Conclusions: In youth soccer players, two weeks of physical training during the off-season improved both physical fitness and core dynamic balance, suggesting that this training is effective for injury prevention.