The academic performance of undergraduates is as a result of several factors involving student- and school-level characteristics. Understanding the effect of these factors is beneficial to both students and the entire institution. The current study examines the relationship between the independent variable (self-concept) and dependent variable (student academic performance) through a proposed mediator (motivation). Correlation design, multiple regression and mediation analysis were employed as the procedures of analyzing our data. The study sample comprises 365 final-year students drawn from arts and science faculties in selected universities based in Kenya. Correlation output revealed that academic performance positively correlated with motivation (r=0.333, P<0.01). Further composite regression analysis revealed a significant influence of motivation ([beta] = 0.97, P<0.001) on academic performance. Mediation analysis identified indirect-only mediation (a × b= 0.049, P < 0.01). Both Sobel z-test and bootstrap results indicated a significant indirect effect a × b while the direct effect C is not significant, thus signaling the presence of indirect-only mediation. Generally, motivation has a mediating role ([beta] = 0.311, r = 0.333) in relation to self-confidence and academic performance. These results imply that students' levels of motivation and self-concept are vital to enhance academic performance.