In 1995, Mexico instituted a new system which provided significantly greater funding to local municipalities. This both offered new opportunities to local leaders as well as it brought significant challenges. Municipal Authorities and also local village authorities (Municipal Agents) took stock of this new reality and of their own initiative sought out training and consulting to better respond to this new situation. In 1999, four Oaxacan Not-For-Profit organizations founded the School for Municipal Leaders. These organizations were CAMPO (Centro de Apoyo al Movimiento Popular de Oaxaca), CESEM (Centro de Servicios Municipales "Heriberto Jara"), EDUCA and UCIZONI. These organizations worked together to provide the training and help which municipal leaders were seeking. From the beginning, the founding organizations oriented the School for Municipal Leaders specifically to address the reality and needs of indigenous municipalities.

The School of Municipal Leaders worked out a specific currículum to respond to the needs of municipal leaders and also provided training to other people and organizations working to aid municipal leaders.

The School continues to operate under the collective guidance of four not for profit organizations: EDUCA, CAMPO, CESEM and Tequio Jurídico.