Muscle strength and balance ability have been related to injury prevention and game actions performance in football. The aims of this study are twofold: (1) to examine bilateral asymmetries in isokinetic strength and balance assessments, and (2) to evaluate the relationship between muscle strength and balance measures. Eighty-eight male adolescent football players were assessed for body composition (InBody 770), isokinetic strength (Biodex System 4 Pro Dynamometer), and balance performance (Biodex Balance System). Paired samples t-tests were conducted to determine bilateral differences in strength and balance. Pearson correlations and multiple linear regression analyses evaluated the relationship between strength and balance. No significant bilateral strength differences were observed in knee flexors (KF) and knee extensors (KE) peak torque (PT) scores. No bilateral differences were found for balance measures, except in the lateromedial stability index, which was better while performing with the preferred leg (p ≤ 0.01; d = 0.29). Significant correlations were found between KE PT and balance tasks (p ≤ 0.01). KF and KE PT shared between 18 and 22% of the common variance in the overall stability index in the non-preferred and preferred leg, respectively. Monitoring strategies of bilateral asymmetries may be crucial to enhance performance in tasks underpinned by unilateral movements, such as changes of direction and sprints, and to identify players at risk of injury. Adopting these strategies during the early stages of football training might be crucial for players’ long-term development.