Wilson made his screen debut portraying characters suspected of murder in his first two films. In his debut film, Wilson played a murder suspect in 1967's In the Heat of the Night, which starred Sidney Poitier, Rod Steiger and Warren Oates. His follow-up role, in the same year, was In Cold Blood, based on the book of the same name by Truman Capote. The film earned Wilson an appearance on the cover of Life Magazine, published on May 12, 1967. Wilson was just 24 years old at the time. Wilson appeared in The Great Gatsby in 1974 opposite Robert Redford. He received a 1980 Golden Globe nomination for Best Supporting Actor for his performance in The Ninth Configuration by director and friend William Peter Blatty. In 1995 Wilson got attention for his role as a prison chaplain in Dead Man Walking, starring Susan Sarandon and Sean Penn, based on the book of the same name by Sister Helen Prejean.

Wilson's long filmography also includes The Gypsy Moths, The Right Stuff, A Year of the Quiet Sun, Malone, The Grass Harp, Junebug, The Host, Monster, Young Guns II, Pearl Harbor, Big Stan, Judge Dredd, the Shiloh film series and Behind the Mask: The Rise of Leslie Vernon. Wilson has filmed on location in South Korea, Japan and Spain. Wilson had a recurring role in several episodes of CSI: Crime Scene Investigation as Sam Braun, father of crime-scene investigator Catherine Willows (portrayed by Marg Helgenberger). Braun was killed off in the episode "Built to Kill, Part 2." In the fall of 2011 he also made an appearance opposite Laura Dern in the HBO series, Enlightened.

Wilson was cast as Dr. Hershel Greene in the second season of The Walking Dead in June 2011. The role has earned him positive reviews, including a "cheer" from TV Guide, which wrote that he had contributed "subtle shades of humanity to the character of Hershel Greene."