This study compares, describes, and analyzes HIV/Aids and Primary Education in Kenya: Effects and Strategies in terms of enrollment, participation, completion and drop-out rates of pupils in selected urban and rural case study schools in two districts, Homa Bay and Murang’a. Special attention has been paid to the gender perspectives, including traditional gender roles and the cultural patterns prevailing around the case school communities. A multi-disciplinary approach has been applied, combining qualitative and quantitative methods and techniques. Particular consideration has been given to the ethical matters related to this study. Information has been collected utilizing techniques such as focus group discussions (FGD), participant and non-participant observation, and interviews. Indications for research, policy, planning, and implementations have been analyzed. Findings suggest that the HIV/Aids pandemic has added numerous challenges to education both at the micro and the macro-levels but more at the micro-level where it affects the individual, a particular household, or a particular community.