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Introduction Menstrual hygiene practices refers to maintaining specific hygiene during menstrual periods. Excused or unexcused school absenteeism can be attributed to adopted menstrual hygiene practices. This study aimed to assess the prevalence of school absenteeism during menstrual cycle and to explore the association of menstrual hygiene practices with school absenteeism among schoolgoing adolescent girls in Bangladesh. Methods A cross-sectional study was conducted from April to November 2019 based on a sample of 442 school-going adolescent girls (aged 10–19 years) from randomly selected nine Girls’ Schools in the Dhaka division, Bangladesh. Data were collected by an interviewer-administered questionnaire and a multiple regression model was applied to assess factors associated with school absenteeism. Results The prevalence of school absenteeism was (35.1%) among school-going adolescent girls in Bangladesh. Factors associated with school absenteeism included older adolescent girls (AOR=2.97; 95% CI: 1.66–5.24, p