Health system strengthening efforts also entails streamlining an existing referral system in a particular context to improve quality of health care offered to people. Conceptually, the referral system in South Africa, is seemingly sound. Nevertheless, gaps exist in its implementation. The aim of this study was toexplorehealth care professionals' perceptions of referral system implementation in the Buffalo City Metropolitan Municipality (BCMM) in the Eastern Cape Province of South Africa. This qualitative study included 12 health care professionals as participants. Each participant was interviewed using a semi-structured interview guide; with their consent, the interviews were audio recorded andtranscribed verbatim. For data analysis, a thematic content analysis was used. The participants identified many impediments to the effective implementation of the referral system in BCCM. The main obstacles were deteriorating infrastructure, inadequate staffing, lack of transportation, and inadequate medical supplies and medications. In mitigation, the participants proposed suggestions such as increasing the capacity of the health workforce, allocating personnel appropriately, increasing the availability of transportation, and providing essential medications to all levels of care. They also suggested involving all stakeholders in the referral process, providing education and training to health professionals on the referral system, and enhancing communication and feedback between the various levels of care. These challenges emphasised in this study highlight the need for targeted interventions to improve the referral system in this setting.