This paper examined internal challenges affecting academic performance of student-athletes in Ghanaian public universities, using a descriptive survey research design. Proportionate random sampling technique was employed to select Three Hundred and Thirty-Two (332) respondents for the study. The instrument used in gathering data for the study was a questionnaire titled "Questionnaire on Internal Challenges Affecting University Athletes (QICAUA)" structured and developed by researchers. The QICAUA was validated by two jurors in the field of physical education and sport, from Ghana and Nigeria and pilot tested using test-retest method. A reliability correlation coefficient of 0.85r was obtained from the reliability testing. In all, two research hypotheses were formulated and tested at 0.05 alpha level of significance. Data collected were analyzed using chi-square (x2 ) statistical method. The findings from the study showed that time constraints and physical/emotional strain were significant internal challenges affecting the academic performance of student athletes in Ghanaian public universities. Based on these findings, the study recommends that Management of universities, university sports administrators and the Ghana Universities Sports Association (GUSA) should collaborate to schedule sports programmes in such a way that student-athletes will have adequate time for both academics and sports; student-athletes should be counselled on how to manage their time effectively on campus; and coaches should ensure that student-athletes are not over worked physically and emotionally during training and competitions.