Poor knowledge and management of menstruation impacts girls' school attendance and academic performance. This paper aims to explore how menstrual hygiene management practices and related factors influence school absenteeism and drop-out among primary and secondary school girls in rural Gambia. Mixed-method studies were conducted among students and key informants from 19 schools from July 2015-December 2017. Focus group discussions, in-depth interviews, cross-sectional surveys, menstrual diaries, and school water, sanitation and hygiene (WASH) facility observations were used. Key findings from the interviews were that menstrual pain, cultural beliefs, fear of peers knowing menstrual status, and poor school WASH facilities led to school absenteeism, however, they had no impact on school drop-out. Of the 561 girls surveyed, 27% reported missing at least one school day per month due to menses. Missing school during the most recent menstrual period was strongly associated with menstrual pain (extreme pain adjusted odds ratio (AOR) = 16.8 (95% CI: 7.29-38.74)), as was having at least one symptom suggestive of urinary tract infection (AOR = 1.71 (95% CI: 1.16-2.52)) or reproductive tract infection (AOR = 1.99 (95% CI: 1.34-2.94)). Clean toilets (AOR = 0.44 (95% CI: 0.26-75)), being happy using school latrines while menstruating (AOR = 0.59 (95% CI: 0.37-0.93)), and soap availability (AOR = 0.46 (95% CI: 0.3-0.73)) were associated with reduced odds of school absenteeism. This study suggests menstrual pain, school WASH facilities, urogenital infections, and cultural beliefs affected school attendance among menstruating girls in rural Gambia.