This research examined how common multiple sexual partnerships are among in-school adolescents and identified factors associated with this behavior. Data were drawn from the 2016 Global School-Based Student Health Survey (GSHS) and re-analyzed to estimate the prevalence and predictors of having multiple sexual partners among 2,496 adolescents aged 13–17 years attending school in Benin. Overall, 26.1% of adolescents reported having more than one sexual partner. In multivariable analyses, being male (AOR = 4.80, 95% CI 3.78–6.09), skipping school without permission (AOR = 1.69, 95% CI 1.35–2.12), physical inactivity (AOR = 1.28, 95% CI 1.00–1.62), cigarette use (AOR = 3.14, 95% CI 1.95–5.07), and alcohol consumption (AOR = 1.78, 95% CI 1.44–2.20) were linked to significantly higher odds of engaging in multiple sexual partnerships. Conversely, younger adolescents (AOR = 0.37, 95% CI 0.25–0.56), students in lower school grades (AOR = 0.52, 95% CI 0.42–0.65), and those experiencing parental supervision (AOR = 0.71, 95% CI 0.55–0.91) showed reduced likelihood of reporting multiple partners. Interventions aimed at reducing unsafe sexual practices should address individual behaviors, school-related factors, and psychosocial influences through integrated, multidisciplinary strategies. Such efforts may support progress toward Sustainable Development Goal 3, target 3.4, which focuses on adolescent mental health and well-being, as well as Goal 4, target 4.1, which emphasizes equitable access to quality education among adolescents in Benin.