Objectives: To determine the effect of a novel low volume high intensity concurrent training regimen and warm-up on physiological performance and musculoskeletal injury in Australian recruits. Design: Controlled longitudinal intervention. Methods: Military recruits completed 12 weeks of either experimental (EXP: n = 78, 6-8RM resistance loads, and high intensity intervals) or basic military (CON: n = 69, usual practice) matched for total sessions and time. Endurance (3.2 km 22 kg-load carriage, V˙O2 peak, multi-stage fitness test (MSFT)), 1RM strength and local muscle endurance (bench, squat, box-lift and push-ups) and power (squat jump) were assessed at Weeks 1,6,12. Body composition, physical activity (PAC·min−1) and heart rate reserve (HRR%), were assessed at Weeks 2,7,9. Musculoskeletal injury and mechanism were recorded. Two-way repeated measures ANOVA interaction (group × time), mean difference and effect size (ES) are reported p ≤ 0.05. Results: A significant interaction over 12 weeks was observed for load carriage (ES −0.30), squat jump (ES 0.65), V˙O2 peak (ES 0.58), MSFT (ES 0.41), push-ups (ES 0.26), 1RM bench (ES 0.26), squat (ES 1.05) and box lift (ES 0.27) in EXP compared to CON. At Week 12 significantly greater squat (38.9 kg), MSFT (2.1 mL·kg−1·min−1), and faster load carriage (49.9 s) was observed in EXP than CON, but no difference in body composition. EXP had a lower PAC·min−1 (641.1 ± 63.1) but higher HRR% (21.8 ± 4.0) compared to CON. EXP had a lower number of injuries (6) compared to CON (17). Conclusions: The inclusion of compound-specific resistance exercise and high intensity intervals improved physical function and was associated with reduced musculoskeletal injury.