The aim of this study was to determine whether the speed, agility, aerobic and anaerobic capacities of football players varied by playing positions. Elite youth football players (n = 123, age = 15.7 ± 0.5 years) who played in six different positions, as goalkeepers (GK), full backs (FB), central defenders (CD), wide midfielders (WM), central midfielders (CM), and attackers (AT), were assessed. Multivariate analysis of variances was used to compare the following variables: Linear running sprint for 5 m (S5) and 10 m (S10), flying sprint for 20 m (F20), agility 505 test with turn on the dominant (A505D) and non-dominant leg (A505N), agility K-test, Yo-Yo intermittent recovery (YYIR1) test and repeat sprint ability (RSA) test. The results showed significant influence of playing positions on linear-running sprint performance (F1,123 = 6.19, p < 0.01, ηp2 = 0.23). Midfielders reached significantly higher performance levels (CM = 2.44 ± 0.08 s, WM = 2.47 ± 0.13 s) in the A505N test compared to GK (2.61 ± 0.23 s). Outfield players had significantly higher performance in both YYIR1 and RSA tests compared to GK (p < 0.01). The results of this study may provide insightful strategies for coaches and clinical practitioners for developing position-specific conditioning programs.