Limited research has been conducted to explore sex differences in biomechanical and physiological demands of the front and back squat, especially in response to fatigue where technique may be altered. Therefore, this study investigated differences in electromyography and force production in performance of back and front squats before and after a fatigue protocol and how this differed between males and females. 35 participants (5 female, 30 male) performed a fatigue protocol for back and front squats with measures of maximal performance pre and post. Main findings were that mean and peak activation of the semitendinosus was greater in the back squat than the front squat suggesting that the back squat has greater hamstring activation possibly for hip stabilisation and knee flexion (p < 0.05). There were no differences in quadricep activation between back and front squats, disputing the notion that front squats have a greater quadricep focus, however, lending support to the hypothesis that quadricep activation equal to the back squat can be achieved with lighter absolute load in a front squat. There were no differences in electromyography as a result of fatigue however force production decreased for back squats following fatigue (p < 0.01). This decrease could result from decreased acceleration out of the bottom position and into the concentric phase. This study also presents preliminary findings of greater mean and peak rectus femoris activation in females compared to males in both front (p < 0.01) and back squats (p < 0.05). This was suggested to be in order to support the knee and in an attempt to prevent knee valgus and excess hip adduction. These findings have implications in programming for both high performance sport and for rehabilitation of lower limb injuries.