Abstract This project is on A comparative analysis of student academic performance in public and private secondary schools in Ondo state. The result obtained revealed that students in private secondary schools in rural areas performed better in Basic Science than their public counterparts. The result obtained also revealed that students in private secondary schools in rural areas performed better in Basic Science than those in public secondary schools in rural areas this is because the majority of 55% had credit pass in private schools whereas few 35% had credit pass in rural public schools. Generally, students in rural areas had low performance when compared to those in urban schools. The low level of students’ performances in rural public schools might perhaps be attributed to what we can describe as poor staffing in schools. Frequent withdrawal of children from school, truancy, the study also agrees with Oke(1992), Adeyemi (1998) and Onipede (2003) that private schools in rural areas perform better. The result of the analysis had shown that male students in both public and private secondary schools in Ondo state outperformed their female counterparts. The result revealed a credit pass of 46.44% and 44.82% male and female students respectively. The result of this study is in line with those of Adhimabi and Heneveld(1995) who observed that male students outperformed the female students academically. However, the result of this study disagrees with the study of Yahaya (2005) who opined that gender analysis of performance is not on biological differences. It is obvious from the results presented above, that pupils in the private Secondary schools performed better than their counterparts in the public schools, lending credence to the earlier study reported (Braun, Jenkins&Grigg, 2006 Lubienski&Lubienski, 2006 and Yoloye, 1988). This, of course, could be attributed to a number of factors.