Background: Running as exercise may be performed either on an outdoor surface or treadmill surface. However, previous research has indicated that the nature of both the surfaces differ significantly and therefore the training outcomes from running in these surfaces may also vary. Aim: Therefore, the aim of this pilot study was to compare the effects of 6-weeks of supervised outdoor running (OT) vs treadmill running (TT) on physical fitness and body composition in recreationally active young males. Methods: Participants (age: 19.82 ± 1.28 years, height: 172.6 ± 4.9 cm, body mass: 64.3 ± 8.7 kg) were randomly assigned to OT (n = 14) or TT (n = 14), and assessed for physical fitness, i.e., 50 m sprint, cardiorespiratory endurance (i.e., 1,600 m run time-trial), standing long jump (SLJ), flexibility (i.e., sit-and-reach test), and upper-body muscle endurance (i.e., push-ups repetitions), alongside body composition, i.e., body mass, body mass index (BMI), fat percentage, fat free mass, and leg skeletal muscle mass (SMM). A two (pre-post intervention) by two (OT, TT) mixed ANOVA analysed exercise-specific effects. For significant group-by-time interactions, Bonferroni adjusted paired (within-group) and independent (between-group comparisons at post) t-tests were used for post-hoc analyses. Results: Significant time-effect was found in all physical fitness variables (all p < 0.001, η2p = 0.67–0.91), body mass (p = 0.23, η2p = 0.18), BMI (p = 0.009, η2p = 0.24), body fat percentage (p = 0.001, η2p = 0.38), and leg SMM (p = 0.002–0.007, η2p = 0.25–0.33). Significant group-by-time interaction was found for 50 m sprint (p = < 0.001, η2p = 0.74), 1,600 m run (p = 0.001, η2p = 0.35), and SLJ (p < 0.001, η2p = 0.43), favouring OT. Group-specific post-hoc tests showed improvements in all physical fitness variables after OT (p = < 0.001–0.001, g = 0.69–2.32, %Δ = 3.0–12.4) and TT (p = < 0.001–0.017, g = 0.15–0.65, %Δ = 0.9–11.7), and fat percentage after OT and TT (p = 0.002–0.041, g = 0.14–0.26, %Δ = 4.3–6.0). However, leg SMM decreased in TT (p = 0.001–0.004, g = 0.14–0.15, %Δ = 6.2–6.7). Conclusions: Both OT and TT improved physical fitness and decreased fat percentage. However, compared to TT, the OT intervention preserved leg SMM and induced greater physical fitness improvements.