Understanding and exploring stakeholders' perceptions and preferences regarding comprehensive sexuality education (CSE) is critical in enhancing programme acceptability. We conducted this qualitative study to explore stakeholders' experiences and preferences of CSE in Kitwe district, Zambia. We employed a qualitative descriptive design within the interpretive paradigm at nine purposefully selected secondary schools. Data were collected through classroom observation, in-depth interviews, and focus group discussions. In depth interviews were undertaken among 21 pupils, 17 teachers, 4 policymakers, 4 parents, and 4 religious leaders. Two focus group discussions were conducted among 14 pupils with each group having seven pupils. Data were analysed using inductive thematic analysis. Interviews continued until data saturation. Our analysis yielded themes on stakeholder experiences of CSE which included: a lack of pupil-centred pedagogy; a lack of stakeholder engagement; a lack of CSE competency and skills; holding back culturally sensitive topics; a lack of guidance from the comprehensive sexuality curriculum; and a lack of CSE prioritisation in schools. Themes on preferences included: the formation of community advisory boards; the need to enhance teachers' professional competencies, linking CSE with community SRH services, pupils SRH needs assessment. A community participatory approach to the design and implementation of a CSE programme is critical in enhancing programme acceptability in schools. While understanding the experiences and preferences of pupils regarding CSE can help determine programme content and priority, improving teachers' competency and skills through appropriate CSE training can help to reconcile teachers' personal beliefs and the content of CSE.