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Gender-based violence remains a critical concern affecting female students in higher education institutions, with significant implications for their academic success, psychological well-being, and overall safety. This protocol outlines a qualitative study designed to explore the experiences of undergraduate female students regarding GBV within HEIs and to develop contextually relevant preventive strategies. The study adopts an interpretive qualitative approach using a phenomenological and exploratory research design to gain an in-depth understanding of participants lived experiences. Purposive sampling will be employed to recruit approximately 15 undergraduate female students aged 18–24 years and four student counsellors as key informants. Data will be collected through semi-structured face-to-face interviews and analysed using thematic content analysis guided by Tesch’s framework. The study is informed by Afrocentricity, African feminism, and empowerment theory, which provide a culturally grounded and intersectional lens for understanding GBV and informing prevention strategies. Trustworthiness will be ensured through credibility, transferability, dependability, and confirmability. Ethical principles, including informed consent, voluntary participation, confidentiality, and anonymity, will be strictly upheld. The findings are expected to generate rich insights into the nature and impact of GBV on female students and to inform the development of evidence-based prevention strategies, including awareness programmes, improved reporting systems, and strengthened institutional support mechanisms.