conducted by the Rivers state ministry of education for junior secondary school three certification. The study attempted to detect differential item functioning of the administered items on urban and rural JSS3 students in Rivers State. A sample size of 240 students drawn from the entire JSS3 population in the state using multistage random sampling technique were used for the study; 120 from urban and 120 from rural schools. Comparative research design was adopted as the framework in this study. The 60 multiple choice 2019 basic science BECE items were used as instrument for data collection which were administered to the students. Items were dichotomously scored. R software was used for item analysis to determine difficulty and discrimination parameters in Two Parameter Logistic Model (2PLM) of Item Response Theory (IRT). R was also adopted to detect deferentially functioning items using Mantel-Haenszel DIF detection method. The study compared results between urban and rural students item characteristic curves, parameters, chi-square statistics, and p-values. It was discovered that urban students found more of the 2019 basic science BECE items easier than their counterparts in the rural areas. The study also revealed that some items deferentially functioned between the two groups when used to assess them. Based on the findings, it was recommended that basic science items for such assessment should be thoroughly checked for DIF, and if found, eliminated or edited before use. Both urban and rural students should be placed on the same condition of learning.