Menstrual hygiene management (MHM) has received increasing attention as a public health issue globally. Governments and stakeholders have started to engage communities to address barriers and challenges faced by adolescents in and out of school. This study, conducted in Siha District, northern Tanzania, responds to the call for evidence sensitive to local barriers and challenges to inform successful strategies in MHM. Institutional-based cross-sectional study which involved 400 school girls aged 10 to 19 years old who attained menarche were randomly selected in four secondary and advanced level government schools from September 2019 to January 2020. Bivariate and multivariable logistic regression analysis were employed. A P-value less than 0.05 was used to declare statistical significance. Among all the girls who participated in the study 30% reported missing school due to menstruation while 56% of the girls reported using toilets as changing places at school. The use of reusable sanitary material was 52% compared with non-reusable materials which was 48%. In urban areas, 34.5% of students reported missing school due to menstruation compared to 25% who reported in rural areas. The findings show that school absenteeism among adolescent girls during menstruation is significantly associated with a headache (Adjusted odds ratio (AOR) = 3.3 (95% CI:1.32-8.23)) and abdominal waist pain (AOR = 8.50 (95% CI: 6.27-15.56)), lack of changing rooms in school (AOR = 5.85 (95% CI: 4.82-7.93)). In addition, the high cost of sanitary pads was mentioned as one of the main reasons for students not using sanitary pads. This study calls for promoting MHM-friendly practices in schools to create a supportive and conducive learning environment for adolescent girls. Ongoing infrastructure improvements such as the construction of classrooms and toilets in schools should include the construction of proper changing places to reduce the number of adolescent girls who miss school due to menstruation.