Church, the fourth of six children, to an Army officer/health care worker father and a telephone company sales rep mother. He was raised under his stepfather's surname, "Quesada", and later changed his surname to "Haden Church". He was raised in Laredo, Texas and graduated from Harlingen High School, Harlingen, Texas in 1979, going on to attend the University of North Texas.
Church started in the entertainment business as a radio personality and doing voiceover work. A part in an independent film convinced him to move to California to pursue an acting career.
He played the part of dim-witted airport mechanic Lowell Mather for six seasons on the NBC sitcom Wings.
After having small roles in films such as Monkeybone and 3000 Miles to Graceland, he made his directorial debut Rolling Kansas in 2003. In 2005, he was invited to join the Academy of Motion Picture Arts and Sciences. On September 16, 2007, he won an Emmy Award for Outstanding Supporting Actor in a Miniseries or Movie for his role of Tom Harte on AMC's Broken Trail.
Church resides on his large ranch in Bandera County, Texas, which he bought in 1998. He and his wife Mia have a daughter named Cody.