Lyon College has retained its denominational affiliation since its founding and is today one of 65 four-year institutions nationwide recognized by the Presbyterian Church as a Presbyterian College. Lyon is one of eight educational institutions that maintains a Covenant with the Synod of the Sun that is periodically reviewed, renewed and affirmed.
The College is governed by a self-perpetuating Board of Trustees that includes one ordained member of the denomination. The College is a member of the Association of Presbyterian Colleges and Universities. It maintains ties to Presbyterian Churches throughout the region, regularly participating in the Kirkin' o' The Tartan worship services that draw upon its Pipe Band and regalia.
In the role of governing bodies of the Presbyterian Church (U.S.A.) and on any institution they serve, the role of Presbyterian clergy is the same as Presbyterian elders. Elected commissioners to the biennial General Assembly meeting must have equal numbers of ministers and elders.