Truancy among in-school adolescents has long been established as a major issue that negatively impacts educational attainment or goals and mental health-related issues. However, research on subjects such as physical education (PE) truancy and its correlates is somewhat limited. This study estimated the prevalence of PE and assessed the factors associated with PE truancy in Benin among in-school adolescents. The 2016 Benin’s Global School-Based Health Survey (GSHS) data from a sample of in-school adolescents (n = 2496; 13–17 years) were used for data analysis. The overall prevalence of past 30-day truancy in PE class was 15.4%, with female adolescents reporting a higher prevalence of PE truancy than their male counterparts. Stratified by gender, the regression analyses showed that males in 3rd–6th grade (aOR = 0.69, CI = 0.50–0.96) experiencing hunger (aOR = 0.51, CI = 0.32–0.81) and having suicidal ideations (aOR = 1.64, CI = 1.07–2.53) predisposed adolescents to PE truant behaviour. For female in-school adolescents experiencing hunger (aOR = 1.75, CI = 1.15–2.65), drinking alcohol (aOR = 0.62, CI = 0.44–0.87), having sedentary lifestyles (aOR = 0.62, CI = 0.40–0.96), and being physically attacked (aOR = 0.53, CI = 0.33–0.87) were significantly associated with PE truancy. However, understanding and supportive parents [aOR = 0.61, 95% CI = 0.41–0.91] was a protective factor against PE truancy. The present findings suggest the design of gender-sensitive school-based interventions to help minimise or prevent PE truancy among in-school adolescents in Benin based on the predisposing factors while emphasising the protective influences.
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