Despite concussion being a serious public health concern and the increasing participation of female athletes in sport, the comparative long-term outcomes of male and female athletes are poorly understood, potentially limiting the scientific understanding and clinical management of these injuries. We examined whether sex influences the long-term cognitive outcomes in athletes with a history of concussion (HOC; 6+ months from injury). Accordingly, 196 asymptomatic student-athletes participated in the study (98 with a HOC; 98 matched controls). The sample included both male (n = 98) and female athletes (n = 98). Participants completed the Cogstate brief battery, to which we added a 2-Back condition to increase cognitive load. As predicted, the results revealed sex differences on the N-back Task, a measure of executive functions, with female athletes having a HOC responding significantly more slowly than their male counterparts on the 2-Back condition (p = 0.02). Moreover, irrespective of sex, athletes with a HOC were slower and less accurate relative to controls on the N-back Task (p = 0.01). Analyses failed to reveal any significant sex or group difference on tasks that measure lower-level cognition (ps > 0.05). The current results reaffirm the presence of subtle, yet long-term alterations in aspects of executive functions following a sport-related concussion. More importantly, our results highlight that female athletes exhibit alterations of greater magnitude than their male counterparts. Therefore, the sex difference observed in the days or weeks following a concussion may persist well into the chronic phase of injury.