El Paso County is governed by a board of county commissioners. Its current members are Holly Williams in district 1, Carrie Geitner in district 2, Stan VanderWerf in district 3, Longinos Gonzales Jr in district 4, and Cami Bremer in district 5.
In 2004, the voters of Colorado Springs and El Paso County established the Pikes Peak Rural Transportation Authority (PPRTA) and adopted a 1% sales tax dedicated to improving the region's transportation infrastructure. Together with state funding for COSMIX (2007 completion) and the I-25 interchange with Highway 16 (2008 completion), significant progress has been made since 2003 in addressing the transportation needs of the area. In 2012, the county voted to legalize marijuana. On March 12, 2019, the county commissioners unanimously passed a resolution to become a Second Amendment sanctuary.
The Colorado Department of Corrections has its headquarters in an unincorporated area in the county.