Objective: The aim of this study was to determine the impacts of anterior cruciate ligament reconstruction (ACLR) and recent (< 12 months) hamstring strain injury (HSI) on (1) future HSI risk, and (2) eccentric knee flexor strength and between-limb imbalance during the Nordic hamstring exercise. A secondary goal was to examine whether eccentric knee flexor strength was a risk factor for future HSI in athletes with prior ACLR and/or HSI. Methods: In this prospective cohort study, 531 male athletes had preseason eccentric knee flexor strength tests. Injury history was also collected. The main outcome was HSI occurrence in the subsequent competitive season. Results: Overall, 74 athletes suffered at least one prospective HSI. Compared with control athletes, those with a lifetime history of ACLR and no recent HSI had 2.2 (95% confidence interval [CI] 1.1–4.4; p = 0.029) times greater odds of subsequent HSI while those with at least one HSI in the previous 12 months and no history of ACLR had 3.1 (95% CI 1.8–5.4; p < 0.001) times greater odds for subsequent HSI. Only athletes with a combined history of ACLR and recent HSI had weaker injured limbs (p = 0.001) and larger between-limb imbalances (p < 0.001) than uninjured players. An exploratory decision tree analysis suggested eccentric strength may protect against HSI after ACLR. Conclusion: ACLR and recent HSI were similarly predictive of future HSI. Lower levels of eccentric knee flexor strength and larger between-limb imbalances were found in athletes with combined histories of ACLR and recent HSI. These findings may have implications for injury rehabilitation.