Management of menstruation can present substantial challenges to girls in low-income settings. In preparation for a menstrual hygiene intervention to reduce school absenteeism in Uganda, this study aimed to investigate menstruation management practices, barriers and facilitators, and the influence of menstruation on school absenteeism among secondary school students in a peri-urban district of Uganda. Girls reported substantial embarrassment and fear of teasing related to menstruation in the qualitative interviews, and said that this, together with menstrual pain and lack of effective materials for menstrual hygiene management, led to school absenteeism. All policy makers interviewed reported poverty and menstruation as the key factors associated with school attendance.