Musculoskeletal injuries (MSIs) are a leading cause of separation from the U.S. Navy. Data have shown that several psychological responses to MSI are associated with treatment outcomes. Yellow flags are maladaptive psychological responses to injury and predict delayed recovery, whereas pink flags indicate resilience after MSI and are associated with good treatment outcomes. Identifying these factors in patients with MSI would permit early targeted care to address factors that may delay their readiness for deployment and enhance factors that support recovery. Active duty service members with MSI who reported to physical therapy outpatient services at a naval hospital were recruited for the study. Yellow flags were assessed at baseline as part of a larger study. Participants completed the Fear Avoidance Beliefs Questionnaire (with two subscales, physical activity and work), the Pain Catastrophizing Scale, and the Hospital Anxiety and Depression Scale. Clinically relevant cut-off scores were used to indicate risk factors of delayed recovery. Pink flags were assessed with the Pain Self-Efficacy Questionnaire and a measure of positive outcome expectations for recovery. Two hundred and ninety participants responded to some or all of the questionnaires. Of these, 82% exceeded the cut-off scores on the physical activity subscale of the Fear Avoidance Beliefs Questionnaire, and 39% did so on the work subscale. Pain catastrophizing exceeded the cut-off in only 4.9% of the sample. Forty-three percent of these exceeded the cut-off for the anxiety subscale of the Hospital Anxiety and Depression Scale; 27% exceeded the cut-off on the depression subscale of the Hospital Anxiety and Depression Scale. Additionally, 54% endorsed scores greater than 40 on the Pain Self-Efficacy Questionnaire, and 53% endorsed a high score on the positive outcome expectations. A substantial portion of the sample endorsed elevated scores on one or more indicators of delayed recovery from MSI. Most participants showed a fear of physical activity, and approximately half reported pain-related distress (anxiety and depression). In addition, feelings of self-efficacy and positive outcome expectations of treatment were endorsed by only about half of the participants, indicating that the remaining half did not report adaptive responses to MSI. Early identification of these risk factors will allow for targeted treatment approaches that incorporate these yellow flags into treatment and support a psychologically informed approach to physical therapy. This approach is likely to reduce delayed recovery and improve deployment readiness.