Background: Low baseline fitness of recruits entering basic military training is shown to be associated with an increased risk of musculoskeletal injuries (MSIs) and attrition of military training. This in turn leads to an increased demand for health care, increased health care costs and decreased personnel occupancy rate of military units. Design: Study protocol for a randomised controlled trial. Objective: To determine the effects of a pre-training conditioning program on cardiovascular endurance, incidence of overuse injuries, and attrition rates in Dutch Airmobile recruits undertaking initial military training. Setting: Royal Netherlands Army, Air Assault Brigade military training course. Participants: Recruits are considered eligible for this study when they are ‘low-fit’ at the start of the initial military training. Time to complete a 2700 m run test in ≥12′23’’ is used as selection criteria. Interventions: We use a complex system approach to cover multiple domains of MSI prevention and optimise intervention circumstance; a pre-training conditioning program, training staff support, process-focused culture and health accountability. The pre-training conditioning program contains functional training to improve mobility, power, agility, lower and upper body strength and cardiovascular endurance. Cardiovascular endurance will be targeted both by endurance training and high intensity interval training. Main outcome measurements: Outcome measures include cardiovascular endurance, injury incidence, attrition rates, lost training days due to injuries, and implementation fidelity of the PCP. Trial status: Recruitment of participants commenced April 18, 2018 and final results are expected in August 2019. Trial registration: Dutch trial register www.trialregister.nl/=trial/6791.