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The New Partnership for Africa's Development (NEPAD) schools were set up as centres of excellence in Information and Communication Technology (ICT) integration, so that other schools could copy their model in e-learning. It was for this reason that they were provided with computers, e-materials, internet appliances and trained personnel. But to gauge their levels of success as e-learning centres there was need to compare them to other schools offering ICT education in Kenya. It was for this reason that this study compared the application of the e-learning in NEPAD and non-NEPAD schools in Kenya. Specifically, the study: Identified significant differences in levels of integration of ICT in curriculum subjects; surveyed the differences in use of e-materials in education research; examined availability of e-libraries; identified significant differences in academic performance of NEPAD and non-NEPAD schools attributed to e-learning. The study used a combination of an exploratory approach using descriptive survey and ex-post-facto design. It was carried out in six of the eight provinces in Kenya, where the NEPAD schools are located. It targeted 1600 form four students from 35 secondary schools involved in ICT education (NEPAD schools included). Saturated sampling was used for the six NEPAD schools while six non-NEPAD schools were selected through simple random sampling. The sample consisted of three officials from the ministry of education, twelve principals and twelve heads of ICT department (HODs), and 570 of the form four students. The main data collection instrument was the questionnaire; administered to the students, the principals, and the HODs. The interview schedule was administered to the ministry of education personnel while an observation checklist was used as a confirmatory tool. Analysis was done using both descriptive and inferential statistics. The study found that, there was a significant difference in the application of e-learning in NEPAD and non-NEPAD schools. Based on these findings, it was recommended that schools involved in ICT education should intensify teacher facilitation and support teacher roles that are required in e-learning Key words: E-Learning, ICT integration, ICT education, new partnership for Africa's development (NEPAD).