Screening for primary musculoskeletal injury (MSK-I) is costly and time-consuming. Both the Functional Movement Screen (FMS) and the Y-Balance Test (YBT) have been shown to predict future MSK-I. With a goal of optimizing the efficiency of primary MSK-I screening, we studied associations between performance on the FMS and YBT and whether history of MSK-I influenced FMS and YBT scores. In total, 365 deploying Marines performed the FMS and YBT as prescribed. Composite and individual scores were each categorized as high risk or low risk using published injury thresholds: High-risk FMS included composite scores ≤14 and right-to-left (R/L) asymmetry for Shoulder Mobility, In-Line Lunge, Straight Leg Raise, Hurdle Step, or Rotary Stability. High-risk YBT consisted of anterior, posteromedial, and/or posterolateral R/L differences >4 cm and/or composite differences ≥12 cm. Pearson's χ tests evaluated associations between: (a) all FMS and YBT risk groups and (b) previous MSK-I and all FMS and YBT risk groups. Marines with high-risk FMS were twice as likely to have high-risk YBT posteromedial scores (χ = 10.2, p = 0.001; odds ratio [OR] = 2.1, 95% confidence interval [CI] = 1.3-3.2). History of any MSK-I was not associated with high-risk FMS or high-risk YBT. However, previous lower extremity MSK-I was associated with In-Line Lunge asymmetries (χ = 9.8, p = 0.002, OR = 2.2, 95% CI = 1.3-3.6). Overall, we found limited overlap in FMS and YBT risk. Because both methods seem to assess different risk factors for injury, we recommend FMS and YBT continue to be used together in combination with a thorough injury history until their predictive capacities are further established.