The organisational structure of SFISM is aligned to functions, with the Rectorate overseeing four sections and a Staff.

As well as teaching plus research and development, the Performance sport, Teaching and sports education and Sports economics sections also offer commercial services. Sports coach education delivers high-quality education and training for Swiss performance and elite sport coaches. The Sport studies organization performs a cross-sectional role across all teaching.

The Rectorate Staff, which also encompasses the media library, the Rectorate Office and a communication service support the Rectorate.