The SCTO has the following members on an institutional level: the five university hospitals, two cantonal hospitals, the SAMS, and the Collège des Doyens. Each member institution delegates a representative to the SCTO Steering Board.
- The Steering Board interacts with a permanent committee composed of the directors of the CTUs, the Board of CTU Directors.
- The SCTO Advisory Board is an independent committee that supports the Steering Board in its strategic decision-making.
- The SCTO Managing Director is responsible for the running of the SCTO Executive Office.
The SCTO is an independent organisation, initially founded in 2009 as a joint initiative of the Swiss National Science Foundation (SNSF) and the Swiss Academy of Medical Sciences (SAMS). As of 2017, the SCTO is a clinical research infrastructure of national importance funded by the State Secretariat of Education, Research and Innovation and the Swiss National Science Foundation.