The aim of the present study was to establish inter-limb asymmetries across different age groups in elite academy male soccer players and to examine any relationships between asymmetry and measures of physical performance. Fifty-one players from an English Premier League soccer academy were split into under-23 (n = 21), under-18 (n = 14) and under-16 (n = 16) groups and performed bilateral and unilateral countermovement jumps, 5, 10 and 20 m sprints and a 505 change of direction speed tests. All tests showed low variability (CV ≤ 2.5%) and good to excellent reliability (ICC = 0.80-0.99). A one-way ANOVA showed that the under-23 group were significantly faster than the under-16 group during the 20 m sprint (2.90 vs 2.98s; p = 0.02; ES = 0.94). No other significant differences were present between groups. Inter-limb asymmetry was quantified from the single leg countermovement jump and no significant differences in the magnitude of asymmetry were present between groups. However, multiple significant correlations were present in each age group between asymmetry and physical performance tests, all of which were indicative of reduced athletic performance. Results from this study show that although inter-limb asymmetry scores are comparable across age groups in elite academy soccer players, differences as low as 5% are associated with reduced physical performance during jumping, sprinting, and change of direction speed tasks. This study suggests the importance of monitoring jump height asymmetries in elite academy soccer players.