Sex-related neuromuscular differences have been linked to greater risk of anterior cruciate ligament injuries in females. Despite this, it remains unclear if sex-related differences are present after injury. This study sought to determine if sex differences are present in the functional roles of knee joint muscles in an anterior cruciate ligament deficient population. An isometric, weight-bearing, force-generation protocol required injured and healthy males and females to modulate ground reaction forces. Electromyography was used to classify the functional role of 10 lower limb muscles in their contribution to knee joint stability during various loading directions. These roles were compared between the four groups at 12 loading directions using a directional analysis. Functional muscle roles were different between groups, except for injured males and healthy females. Healthy males had either joint actuators or specific joint stabilisers, but no general stabilisers; the vastus medialis and lateralis of injured males and healthy females were classified as general stabilisers while injured females added the gluteus medialis and medial gastrocnemius as general stabilisers. A population-based hierarchy in functional muscle roles was discovered. Healthy males demonstrated the most specific muscle roles, which can be viewed as more adaptive to variable loading conditions. The more generalised stabilisation strategies seen in injured males and females would alter joint loading which may be detrimental to the knee joint health over time. In summary, (1) these injuries alter muscle roles; (2) these alterations are sex-specific; (3) rehabilitation might be optimised if sex-differences are considered. •Sex influences neuromuscular control in a healthy population.•Sex influences neuromuscular control after an anterior cruciate ligament injury.•A population-based hierarchy in knee stabilisation strategy was identified.•Rehabilitation programs should consider sex-specific muscle function after injury.