This work is a comparative study of JSCE results between the 6-3-3-4 system (2006 & 2008) and the 9-3-4 (UBE) system (2009 & 2011) in Port Harcourt using a comparative/evaluative survey design. A cluster sampling technique was used to compose a sample of 2,487 drawn from the population of 17,139 candidates in 2006, 2008, 2009 and 2011 in government owned secondary schools in Port Harcourt LGA. Five research questions and hypotheses were formulated to guide this study. The grades of the students were obtained from, the Rivers State ministry of education using a data collection form designed by the researchers. The grades were converted to raw scores and then to T-scores. The research questions were answered using mean and standard deviation hypotheses were tested at 0.05 Alpha level. The results showed that: there was a significant difference between the JSCE results of Mathematics and integrated science in the two systems of education. The results implied that educational systems significantly influence student's performances in the Junior Secondary Certificate Examination.