Background: Emergency Departments (EDs) can serve as clinical sites for identification of new HIV infections and their entry into care. We examined if HIV-positive patients who present to EDs in South Africa are able to successfully link to care. Methods: We conducted a one-year longitudinal prospective cohort study in four hospitals across the Eastern Cape, South Africa between July 2016 and July 2018. All adult, non-critical patients presenting to the ED were systematically approached, asked about their HIV status, and, if unknown, offered a point-of-care (POC) HIV test. All HIV-positive patients were further consented to participate in a follow-up study to assess subsequent linkage to care and distance from “home” to ED. Linkage to care was defined as self-reported linkage (telephonic) or evidence of repeated CD4/viral load testing in the National Health Laboratory System (NHLS) at either 6- or 12-months post index ED visit. Findings: A total of 983 patients consented to participate in the study. In the 12 months following their ED visit, 34∙1% of patients demonstrated linkage to care (335/983), 23∙8% did not link to care (234/983), and 42∙1% (414/983) were lost to follow-up. Though not statistically significant, a higher percentage of young men and those presenting with a trauma-related complaint did not link to care. A considerable proportion of patients (105/454, 23∙2%,) resided 50 or more km from their index ED sites, though there was not a significant difference in linkage to care rate between those who lived closer or further from the ED. Interpretation: Innovative implementation strategies are required to overcome patient-level factors and structural barriers within the health system to improve HIV care linkage to care for both known HIV-positive and newly diagnosed HIV-positive ED patients. Strategies should consider the use of facilitated linkage using case management approaches and same day ART initiation, amongst others. Funding Information: This research was supported by the South African Medical Research Council, the Division of Intramural Research, the National Institute of Allergy and Infectious Diseases, National Institutes of Health, and the Johns Hopkins Center for Global Health. The funding bodies had no role in the design of the study and collection, analysis, and interpretation of data and in writing the manuscript. Declaration of Interests: The authors have nothing to disclose. Ethics Approval Statement: The study was approved by the Johns Hopkins University School of Medicine Institutional Review Board (IRB00105801), the Human Research Ethics Committees (HREC) of University of Cape Town (Ref 856/2015), and the Walter Sisulu University HREC (Ref 069/15). Written consent was obtained from all participants for the collection of demographic data and POC HIV testing.