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Introduction: To address the unmet sexual and reproductive health (SRH) needs of adolescents, the South African government introduced various policies and programs, including the recent Integrated School Health Policy (ISHP). This policy provides students with comprehensive health services, including screenings for pregnancy, STIs, and HIV, as well as education on menstruation, safe sex, and contraception. School health practitioners are responsible for implementation of the ISHP, yet little is known about their perspectives regarding the SRH issues faced by learners. This study aimed to explore the SRH challenges that secondary school learners’ face, the contributing factors for these challenges and possible solutions to deal with these challenges from the perspective of school health practitioners.

Methods: We used an exploratory and descriptive qualitative research design to provide an in-depth understanding of the SRH challenges that secondary school learners encounter. In-depth interviews were used to collect data from school health practitioners comprising eleven Life Orientation (LO) teachers and four school health nurses. All the interviews were analysed using thematic analysis.

Results: School health practitioners perceive high unplanned teen age pregnancy, sexual abuse and lack of adequate knowledge of the symptoms of STIs as key SRH issues requiring attention among learners. Inadequate human resources hinder school health nurses from meeting the demands of screening and providing quality SRH services to learners. Perspectives of LO teachers suggested that they were insufficiently equipped to deliver the LO content. They pointed out a need for adequate training and provision of adequate teaching resources. Parents were highlighted as important stakeholders to be actively involved in the implementation of the ISHP.

Conclusions: The perspectives of school health practitioners are important in the delivery of the ISHP as they identify the implementation challenges they encounter daily as well as the SRH challenges affecting learners. Addressing these challenges can contribute to the effective implementation of the Integrated School Health Policy.