Menstruation-related school absenteeism significantly affects girls’ academic progress and general wellbeing. This study aimed to assess menstruation-related school absenteeism in an urban population in the Northern Region of Ghana. A school-based cross-sectional study was conducted to determine the prevalence of school absenteeism among girls using a structured questionnaire, which was pretested. The data were analyzed using Stata 16. Descriptive and inferential statistics, including cross-tabulation, the chi-square test, and binary logistic regression, were performed. The majority (59%) was between the ages of 15 and 19 years. Approximately one fifth of all respondents missed school during menstruation. Reasons assigned to missing school were menstrual pains (57%), stained clothes (43%), heavy bleeding (40%), and self-stigmatization (2%). The majority (95%) of respondents used some form of materials to absorb menstrual blood. About 88% of respondents used sanitary pads, 11% used cloth, and 1% used tissues to absorb their menstrual blood. The multivariable analysis showed that school girls < 15 years old (AOR: 3.69, 95% CI: 2.02–6.73), first year of Junior High School (AOR: 4.68, 95% CI: 2.14–10.22), and public school (AOR: 3.57, 95% CI: 1.83–6.94) were associated with increased odds of menstruation-related school absenteeism. Menstruation-related school absenteeism is considered high and could affect girls’ educational attainment. School absenteeism due to menstruation, particularly in public schools, warrants attention by the Ghana Education Service.