This study aimed to compare the effects of non-sport-specific and sport-specific training methods on physical performance and perceptual response in young football players. Seventy-nine under 11 participants were selected and assigned to non-sport-specific (NSSG), sport-specific (SSG), and control (CNTG) groups. The NSSG training protocol consisted of combined stimuli based on balance, agility, and jump rope drills. The SSG training protocol included technical exercises, defensive and offensive game-based drills, and a small-sided game. The CNTG included the participants not taking part in any sport training. All participants were tested for general motor coordination (Harre test), dynamic balance (Lower Quarter Y-balance test), and dribbling before and after 10 weeks of training (NSSG and SSG) or habitual activity (CNTG). At post-intervention, perceived enjoyment was requested by the Physical Activity Enjoyment Scale (PACES). A two-way repeated measure analysis of covariance was used to detect interactions and main effects of time and groups controlling for baseline values. Whereas, a one-way analysis of variance was used to evaluate PACES-related differences between groups. NSSG gained greater improvements (p < 0.05) compared with SSG in the Harre and Lower Quarter Y-balance tests, while dribbling skills improved similarly in both groups. Regarding PACES, NSSG and SSG presented a comparable perceived enjoyment. These findings suggest that a 10-week non-sport-specific training is an enjoyable practice capable to promote greater improvements in general motor coordination and dynamic balance compared with sport-specific training in youth football players. This can occur without impairment of football-specific skills.