Despite dynamic efforts from education stakeholders to ensure gender equality in education, there remains a serious gap between boys’ and girls’ academic performance in secondary schools. The studies focusing on the issues of gender difference in academic motivation of students are also scarce in Kenya. This is despite that academic motivation is a significant determinant of academic success of students at any age. This study sought to examine gender differences in the academic motivation of students in public secondary schools in Nairobi County, Kenya. The study employed Self-determination theory by Ryan and Deci. The Academic Motivation Scale, a high school Version was adapted to measure academic motivation. The study adopted a correlation research design. Questionnaires were administered to a sample of 397 form four students drawn from 12 public secondary schools in Nairobi County. Gender difference in academic motivation was tested using Independent Samples t-Test and the level of significance in rejecting the null hypothesis was at p= ≤ .05. The research findings showed gender difference in academic motivation in favor of girls (t= 3.74, df= 318, P< 0.05. This might imply that preferential affirmative action for girls has been effective. A major recommendation of the study was that intervention designs that offer support in initiating, increasing and sustaining students’ academic motivation should be reframed, reviewed and revamped, and especially those that target the boy child. This may ensure equity in performance for all.