The history of EMESP Tom Jobim started back in October 1989. The dean and first president of the council was composer Antonio Carlos Jobim. For a long period of time, the institution was known as the Free University of Music (ULM) and its headquarters were located on the Bom Retiro neighbourhood. In 2001, activities were transferred to the Luz building, then the school was renamed Centre for Musical Studies Tom Jobim and eventually it received its current name: the Tom Jobim School of Music – EMESP Tom Jobim.

In 2009, the Social Organization Santa Marcelina took over the administration of the School. Many an improvement was carried out in the facilities, as well as improvements in labour relations (hiring currently temporary teachers and holding selective processes for hiring new teachers on full time labour law abiding contracts) and the structuring of a new pedagogic proposal focused on instrumental classes and collective practice of music.