Background: Those who are homeless are more prone to communicable, respiratory and cardiovascular diseases and are less likely to access healthcare services. In South Africa there are no specific public healthcare services tailored to the needs of these communities, particularly if they are immigrants. Trinity Health Services is a studentrun inner-city clinic providing free healthcare to the homeless of Johannesburg, South Africa. The clinic operates two nights per month and provides treatment for mainly acute conditions. The purpose of this study was to determine the costs of establishing and operating a student-run clinic for an indigent population. Methods: This costing analysis used a mixed-methods approach combining an ingredients-based and top-down methodology. The costs, capital and recurrent, pertaining to the establishment and operating of the clinic as well as the cost of treatment per patient were identified and quantified from 1st January 2016-31st December 2017. Results: The capital costs incurred in establishing the clinic were calculated to be £10,968.57 (ZAR 214157.08) and included building alterations, equipment purchased, installations, furniture, application for a pharmacy license, consumables and medications. The recurrent costs per annum were estimated at £17,730.72 (ZAR 346185.54) and comprised of overheads and maintenance, rental, personnel, pharmacy license, consumables and medication. The cost of treatment per patient, included medication dispensed and consumables used in the consultation, was estimated at £3.54 (ZAR 69.05) per visit. Conclusions: This study summarised the costs of establishing and operating a student-run clinic providing pertinent information essential to the sustainability of the service. It also provides a model for costs associated with free clinics in faith-based and university settings.