Bone stress injuries (BSI) are common in military trainee populations and can significantly disrupt training given their prolonged healing times. The epidemiology of military BSI is largely based on enlisted basic training. Our objective was to describe the incidence, risk factors, and diagnostic imaging of BSI during the 6-week Basic Cadet Training program at the U.S. Air Force Academy, Colorado, over two iterations (2022 and 2023). The cadet physical therapy clinic assessed all suspected BSI according to a published algorithm and collected information on suspected BSI in a standardized database, including information on established risk factors for BSI in military training. A total of 2211 persons participated in U.S. Air Force Basic Cadet Training during the surveillance period. Physical therapists assessed 132 suspected BSI cases. Of these, 50 were confirmed on imaging, yielding a cumulative incidence of 2.26% and an incidence density of 3.77 BSI per 1,000 person-weeks. Incidence was nearly three times higher among females (7.10 per 1,000 person-weeks) than males (2.43 per 1,000 person-weeks). Several risk factors were commonly reported among those with an imaging-confirmed BSI: an abrupt increase in weight-bearing physical activity in the two months before arrival (96%); history of participation in non-impact sports (42%); history of BSI (38%); and poor baseline cardiorespiratory fitness, defined as an initial 1.5-mile run of 14 minutes or longer (22%). All suspected BSI cases had a plain film radiograph, and 68 had an MRI. Twelve BSI cases were confirmed via plain film, and an additional 38 were confirmed via MRI. Using clinical suspicion as the criterion (“gold”) standard, plain film radiograph had a sensitivity of 9% and MRI had a sensitivity of 74%. Over 30% of cadet basic trainees who presented with a suspected BSI and who had a negative plain radiograph had a BSI observed on MRI. These findings suggest two actions that may prevent BSI and mitigate their impact during Basic Cadet Training: (1) early notification of acceptance with gradual ramp-up of weight-bearing physical activity in the months prior to arrival and (2) the importance of MRI during the initial diagnostic workup of suspected BSI to avoid delays in treatment and recovery.