Background and Objectives: The United Nations’ 2030 Agenda, consisting of 17 main goals, serves as a roadmap for addressing the most pressing global issues. Given the critical role medical sciences universities play in accomplishing sustainable development goals, this study aims to identify the opportunities and challenges that medical sciences universities are facing towards achieving these goals. Materials and Methods: The current qualitative study was conducted in 2021 at Iran's medical sciences universities in an exploratory approach. Up to the saturation point, 38 managers and specialists from various vice departments participated in targeted, semi-structured interviews. The traditional content analysis method developed by Graneheim and Lundman was used to analyze the data. Results: The universities of medical sciences have 25 opportunities to accomplish the goals of sustainable development in four areas: investment, human resources, service provision, and communication and coordination. The 35 challenges are divided into five categories: human resources, service delivery, monitoring and control, cooperation and interactions, and financing. Conclusion: According to the results of the current study, investing enough in primary health care (PHC), utilizing modern systems and equipment, particularly in data recording, hiring and retaining experts in a variety of fields, using appropriate and sufficient incentives, and fostering relationships between vice-chancelleries and medical sciences universities and other organizations are all recommended to meet the goals of sustainable development.