For each PhD prepared in the cotutelle scheme, the partner institutions enter into a separate Agreement on the co-supervision of the dissertation, which sets out the conditions, time schedule, and other requirements for studies and the defence of the dissertation. It is signed by the PhD student and their supervisors, the dean of the faculty, the rector of Charles University and the relevant representatives of the partner institution.

The PhD student is enrolled at both partner universities in accordance with the valid rules and regulations and has all of the corresponding academic rights and obligations. The provisions in the concluded agreements should help prevent any administrative and procedural complications. It must not be in contradiction with the valid regulations for PhD studies in either country and at the respective universities and faculties.

Universities abroad approach the conclusion of agreements on the co-supervision of dissertations differently, and therefore, there may be partial formal and content modifications to the individual agreements.