The aim of this study was to compare the biceps femoris long head (BFlh) architecture between football players with (twelve) and without (twenty) history of BFlh injury before and after a repeated sprint task. Fascicle length (FL), pennation angle (PA) and muscle thickness (MT) were assessed at rest and in the active condition before and after the repeated sprint protocol. Athletes with previous BFlh injury showed shorter FL at rest (p = 0.014; η2p = 0.196) and active state (p < 0.001; η2p = 0.413), and greater PA at rest (p = 0.002; η2p = 0.307) and active state (p < 0.001; η2p = 0.368) before and after the task. Intra-individual comparisons showed that injured limbs have shorter FL at rest (p = 0.012; η2p = 0.519) and in the active state (p = 0.039; η2p = 0.332), and greater PA in passive (p < 0.001; η2p = 0.732) and active conditions (p = 0.018; η2p = 0.412), when compared with contralateral limbs. Injured players, at rest and in the active condition, display shorter BFlh FL and greater PA than contralateral and healthy controls after repeated sprints. Moreover, the BFlh of injured players presented a different architectural response to the protocol compared with the healthy controls.