McDowell had a difficult childhood. His father was an alcoholic. When he was six years old, his parents hired a man by the name of Wayne to work on the farm as a cook and a housekeeper. In an interview with CBN News, McDowell said, "Wayne began molesting me within weeks after he started working for my family.” From age six to 13 years of age, for seven years, every week he was homosexually raped. "It almost destroyed everything in my life." said McDowell.
As a teenager, he was an agnostic, an atheist by default, who felt that Christianity was worthless, but when challenged to intellectually examine the claims of Christianity, he realized its truth and converted, and has since forgiven Wayne.
He attended Kellogg College and Wheaton College, which conferred a Bachelor of Arts degree on him. He also has a Master of Divinity degree from Talbot Theological Seminary of Biola University, La Mirada, California.
Though most of McDowell's publishing has been in the apologetics realm, he also co-wrote with Ed Stewart a series under the title "Project 911 Connection," the series featured small booklets aimed at youth dealing with contemporary issues (such as unplanned pregnancy, childhood sexual abuse, and thoughts of suicide).