There is a knowledge gap concerning the occurrence of physical complaints/injuries, i.e., musculoskeletal disorders (MSD), among Swedish women who undergo basic military training (BMT). The aims were to describe prevalence and factors related to MSD and explore physical exposure and performance in Swedish female recruits during BMT. A total of 144 females (mean age 22 years) who underwent BMT in 2016 participated in this cross-sectional study. Data regarding self-reported MSD, physical performance, physical activity and exercise, motivation and mental and physical preparation, and physical exposure during BMT and perceived health were collected at the end of BMT through the Musculoskeletal Screening Protocol questionnaire. Additional data on muscle strength were retrieved from IsoKai isokinetic lift tests. Descriptive and analytic (paired samples t-test and logistic binary regression) statistics were used. The prevalence of MSD was high, with 33% (n = 48) reporting MSD before BMT, 78% (n = 113) during, and 50% (n = 72) at the end of BMT. Knee and upper back were the most frequently reported MSD locations. Forty-four (30%) participants felt insufficiently physically prepared for BMT. The physical exposure was high with loaded marches/runs and carrying heavy loads as the most demanding tasks. The longest walking distance was reportedly 55 km, and the reported maximum load was 50 kg. Forty-five participants (31%) had carried a load representing over 50% of their body weight. Most participants reported good to excellent health at the end of BMT. There was a small (8 N) but significant (P = 0.045) increase in mean force over time. Two variables, MSD before BMT (odds ratio 2.24, P = 0.03) and being physically unprepared (odds ratio 3.03, P < 0.01), were associated with MSD at the end of BMT. This study showed that the prevalence of MSD in Swedish female recruits was high before, during, and at the end of BMT, with knee and upper back as the most frequent locations. Although the physical exposure during BMT was occasionally high, self-rated health was mainly perceived as good to excellent at the end of BMT. Previous MSD and being physically unprepared were related to MSD at the end of BMT. These important and relevant findings indicate the necessity for implementing interventions to increase physical fitness and treat MSD at the beginning of BMT.