The New York State Federation of Secondary School Athletic Associations was created in 1964 as a collective to exchange ideas among the four high school athletic associations: the Public School Athletic League (New York City), Catholic High School Athletic Association, Association of Independent Schools, and the New York State Public High School Athletic Association.  At the time, state championship events were not being conducted as a result of a 1932 decision by the NYSPHSAA to suspend championships indefinitely, so the emphasis was on best practices for rules enforcement and encouraging participation at the local levels.

At a meeting in April 1973, the Federation representatives began discussing a return to championship play. The NYSPHSAA had recently passed a referendum permitting a return to postseason tournaments, and the Federation considered their options. In April 1974, the NYSPHSAA Central Committee voted to allow Federation association member schools to compete against one another without prior approval, setting the stage for Federation-sponsored events. The first Federation Cross Country Championship was held in 1975, and in the same year the NYSPHSAA allowed Federation association schools to enter into individual state championship events. By 1979 the Federation conducted their first boys basketball championship, then called the Super Sixteen Tournament, and a girls tournament was added in 1982.

In April 1988, the Federation approved a voting procedure that allowed three representatives per association to have voting privileges at meetings. Proxies were approved in the event a voting member was unable to attend. 

In 2007, the Federation appointed Walter Eaton as the first Executive Secretary. This allowed the Federation to operate more independently while still receiving support from the member associations. By September 2008, the Federation became incorporated as the New York State Federation of High School Athletic Associations, Inc. The NYS Federation now crowns champions at ten events each year.
 
This record was compiled in part thanks to Walter Eaton's book on the history of the NYSPHSAA.