Introduction Poor sexual and reproductive health (SRH) is a global public health concern, particularly among adolescents. While school health services (SHS) play a crucial role in preventative care, professionals are inconsistent in addressing SRH issues. This study explored school health professionals’ (SHPs) experiences of an implementation of structured assessments of sexual health and experiences of violence among youth in Sweden using the SEXual health Identification Tool (SEXIT).Methods A qualitative sequential study was conducted from October 2023 to January 2024 to explore the experiences of 57 SHPs trained in the SEXIT method. Data collection included a questionnaire with open-ended questions, group discussions and individual interviews, analysed using qualitative content analysis.Results Addressing sexual risk taking and violence was considered a priority to help youths make informed SRH choices. SEXIT aided SHPs in acting as educators to promote SRH and freedom from violence, normalised conversations about sensitive topics, facilitated the identification of students needing support, and could be integrated as a routine part of preventive work within SHS. However, hindering factors for effective implementation included a lack of supportive leadership and a unified approach among involved organisations to clarify roles, responsibilities and referral pathways. Furthermore, it is essential to further adapt SEXIT and train SHPs to meet the specific needs of vulnerable youths and perpetrators, ensuring equitable support.Conclusions SEXIT offers unique opportunities for SHPs to discuss SRH and violence with school youths, a priority part of their preventive work; however, it is not routinely used, underscoring the need for supportive leadership and a unified approach among organisations.