The Faculty of Medicine's closest collaborator is the University Hospital Münster [de] (UKM); the hospital supports the faculty's research and teaching and is responsible for patient care. The scope of endeavours undertaken by these two institutions are closely intertwined by shared subject matter, personnel and location.

• The scientists within the Medical Faculty work intensively with colleagues in other departments of the University of Münster. For example, the Centre for Molecular Biology of Inflammation (ZMBE) sustains a fruitful and long-term cooperation with the Faculties of Biology, Chemistry and Pharmacy. In addition, collaborative research projects link the Faculty of Medicine with the Faculties of Mathematics and Computer Science, Physics as well as History/Philosophy, Psychology and Sports Science.
• Traditionally, the Faculty of Medicine and the Max Planck Institute for Molecular Biomedicine in Münster maintain an intensive cooperation. Examples include numerous joint research projects as well as the joint graduate program of the Cells-in-Motion Cluster of Excellence and the Max Planck Institute.
• In a public-private partnership, the Department of Neurology with Institute for Translational Neurology collaborates with the biotechnology company Amgen; the interfaculty European Institute for Molecular Imaging cooperates with Siemens Healthineers.

Numerous institutes and clinics within the Faculty of Medicine belong to competence and cooperation networks that focus on specific topics – the following are examples:

• KKS-Netzwerk e. V. [de] – network of clinical trial coordination centres
• Competence Network Multiple Sclerosis
• Medical Informatics Initiative Germany (HiGHmed Consortium)
• German National Cohort / NAKO Health Study
• Nano-Bioanalytik-Zentrum Münster
• German Research Platform for Zoonoses
• TMF - Technology, Methods, and Infrastructure for Networked Medical Research
• Collaborating Centre of the World Health Organization (WHO) for the study of human fertility

The Faculty of Medicine is also nationally and internationally active in teaching:

• The Faculty of Medicine cooperates with universities in Belgium, Denmark, Great Britain, Finland, France, Greece, Italy, Latvia, the Netherlands, Austria, Poland, Portugal, Switzerland, Slovakia, Spain, the Czech Republic, Turkey and Hungary within the framework of the Erasmus program [de] of the European Union which coordinates and promotes studies abroad.
• In non-European countries, cooperations exist between universities in Mexico, Japan and the USA, which allow students the opportunity for exchange semesters.
• The Faculty of Medicine is a partner in the international training research network LOOOP. In the related web portal "Learning Opportunities, Objectives and Outcomes Platform" (LOOOP), medical faculties in Europe, Africa and Asia organize, evaluate and develop their curricula as well as supplement education curricula.
• To ensure transparency and equality in the nationwide allocation of training positions for medical students during their clinical internship year (PJ), the following universities work together: Berlin, Bochum, Bonn, Düsseldorf, Erlangen, Göttingen, Halle/Saale, Jena, Kiel, Munich, Münster, Oldenburg, Rostock and Würzburg. To this end, they utilize an online platform designed and operated in Münster known as the PJ-Portal [de].