Horton hosts Antiwar Radio for Pacifica Radio's KPFK 90.7 FM in Los Angeles, as well as the podcast The Scott Horton Show. Horton has conducted over 5,000 interviews since 2003. He is also the director of the Libertarian Institute.

Horton is the editorial director of the non-interventionist news portal Antiwar.com. He was previously the host of Say It Ain't So on Free Radio Austin 97.1 FM, the Weekend Interview Show and the KAOS Report on Radio KAOS 95.9 FM, for which he won The Austin Chronicle's Best of Austin award in 2007 for "Best Iraq War Coverage".