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Menstrual stigma, characterized by negative beliefs, attitudes, and practices surrounding menstruation, often leads to the social exclusion and discrimination of menstruators. The intersection of menstrual stigma and period poverty, which is marked by limited access to menstrual hygiene products and safe sanitation has a profound impact on the mental health and well-being of adolescent girls, particularly in low- and middle-income countries. This study aimedto examine the associations between menstrual stigma and mental health (Mood and Feelings Questionnaire) among female adolescents aged 10-20 in primary schools in Panyijar County, South Sudan. Cross-sectional baseline data were analyzed from a school safety evaluation using unadjusted and adjusted linear regression models In unadjusted analyses, knowing whether female classmates had their period was significantly associated with poorer mental health (β = 1.75, p < 0.001). Feeling ashamed if boys knew about one's period was also associated with poorer mental health (β = 1.49, p = 0.05). In individually adjusted models, ajusting for demographic characteristics, feeling the need to hide one's period was associated with better mental health (β = -1.80, p = 0.02). In fully adjusted models, which included all stigma variables and demographic controls, hiding one's period remained significantly associated with mental health (β = -1.99, p = 0.04), while knowing when a classmate had their period showed a marginal association with poorer mental health (β = 0.88, p = 0.08). Disability was significantly associated with poorer mental health (β = 2.52, p < 0.01), while displacement showed a marginal association (β = 0.84, p = 0.06). No other demographic variables retained significance. These findings highlight the need for comprehensive strategies that address menstrual stigma and its impact on mental health, including interventions that challenge harmful social norms, promote safe latrine environments, and ensure access to hygiene products and menstrual education.