An increasing number of studies have found that girls in low-income settings miss or struggle at school during menstruation if they are unable to manage their menstrual hygiene effectively. This study explores the menstrual hygiene practices and knowledge of girls at rural government primary schools in the Rukungiri district in Uganda and assesses the extent to which poor menstrual hygiene management (MHM) affects their education. The study concludes that it is common for girls who attend government-run primary schools in the Rukungiri district to miss school or struggle in lessons during menstruation because they do not have access to the resources, facilities, or information they need to manage for effective MHM. This is likely to have detrimental effects on their education and future prospects. A large-scale study is needed to explore the extent of this issue.