Purpose: We assessed the reliability of fundamental movement skills in young male footballers within one session. Methods: 197 players from 5 English category 3 football academies across U9–U18 age groups volunteered (mean: age = 12.6 ± 2.8 years; stature = 156 ± 17 cm; weight = 47 ± 15 kg; years from peak height velocity (PHV) =–1.1 ± 2.3). Motion tracking of squat depth and anterior Y-balance test maximum reach was recorded. Reliability was assessed (trial 1 vs. 2; trial 2 vs. 3) via mean change, intraclass correlation coefficient (ICC), and typical error. Results: The overall mean change was trivial (−1.8–2.9%), while Y-balance left showed a small negative change (trial 2 vs. 3; −3.2%). All ICCs across the tests ranged from moderate to high (0.71–0.79). Typical errors for Y-balance tests ranged from 8.3–10.8% and squats from 19.3–21.8%. Pre-PHV vs. post-PHV players had similar typical errors for Y-balance left and right (9.0 vs. 11.5%; 9.0 vs. 7.1%, respectively), and the squat (21.1 vs. 20%). Conclusions: The high within-player typical error scores obtained over three trials suggest that, contrary to some movement screening guidelines, prior habituation is needed to increase both the stability and reliability of these tests.