The study looked at gender as it relates to academic performance of students in Agriculture Primary School Leaving Examination in Gaborone schools. The research was quantitative ex-post facto type design. The sample composed of 3781 (1751 males and 2030 females) students who wrote PSLE in 2012. The sample was taken from 43 primary schools in Gaborone area which included private and government schools. The results which included students’ scores were obtained from Botswana Examinations Council academic records and were not manipulated in any way. The results were then subjected to testing using Statistical Package for Social Sciences at significance level of 0.05. An independent t-test was conducted to determine significance difference and value of -5.964 which is statistically significance (P = 0.00) obtained and therefore the null hypothesis that states that there is no significant difference between males and females was rejected. The analysis revealed that girls performed better than boys and moreover there is a significant difference between males and females’ academic performance. It was therefore, recommended that the Gaborone Regional Education office intensify research to establish how other variables such as location, parental support and economic status of parents contribute to poor Primary School leaving Examinations.