This paper presents a novel Multiple Criteria Decision Making methodology for assessing and prioritizing medical tourism destinations under uncertainty. A systematic evaluation and assessment approach is proposed by incorporating analytic hierarchy process and multi‐attributive border approximation area comparison methods in the rough environment. Rough number is used to aggregate individual judgements of decision makers and express their true perception to handle vagueness without any prior information. Rough analytic hierarchy process analyses the relative importance of criteria based on their preferences given by experts, whereas rough multi‐attributive border approximation area comparison evaluates the alternative sites based on the criteria weights. A case study of prioritizing different sites (cities) in India for medical tourism services is shown to demonstrate the applicability of the proposed method. Among different criteria “quality of infrastructure of healthcare institutions” is observed to be the most important criteria in our analysis, followed by “supply of skilled human resources and new job creations” and “Chennai” is found to be the best medical tourism site in India. Finally, a comparative analysis and validity testing of the proposed method are elaborated, and the methodology provides a standard for select medical tourism sites on the basis of different criteria.