The FAO of the UN recognizes food-based systems as a platform to address the cornerstones of sustainable development: learning, nutrition, and income. Food security has a strong relationship to primary education and as access to primary education increases, food insecurity decreases. This study measured the impact of a school garden program on agriculture learning of pupils living in a food insecure region of rural Uganda and aimed to identify if the pupils acquire agriculture knowledge and skills through a school garden program. Agriculture learning of pupils attending a school with a school garden program or attending a school without a garden was investigated through three methods: 1) analyzing exam scores of pupils completing primary school grade 7 from two schools, 2) evaluating pre- and post-test scores over an agriculture topic taught in the national curriculum, and 3) administering a questionnaire of pupils. Primary Leaving Exam scores showed improvement at NPS in the period after implementation of the school garden and decreased in the school without a school garden program. Differences in pre- and post-test achievement were not found between schools; however gender was found to have an impact on achievement. The survey results of 64 children identified themes in gender, age, prior garden experience, and school experiences, which play an important role in pupils' learning of agriculture. These investigations enhance our understanding of a school garden program's impact on the learning of agriculture topics at the primary school level in rural Uganda and may be used to identify methods to improve primary education, thereby improving nutrition and promoting food security.