Another short-lived series in which Thinnes starred was The Psychiatrist, in the title role of the unconventional psychiatrist, Dr. James Whitman. The pilot for the series, a TV movie called The Psychiatrist: God Bless the Children (also known as The Psychiatrist: Children of the Lotus Eaters) co-starred Pete Duel in the role of Casey Poe, a former drug addict and patient of Whitman.
He also appeared as intrepid writer and investigator of the supernatural David Norliss in 1973's The Norliss Tapes, a pilot for an unproduced TV series. He also played a suspicious schoolmaster in the TV movie Satan's School for Girls with Kate Jackson.
During the 1982-1983 season, Thinnes appeared on the hit CBS prime time soap opera Falcon Crest as Nick Hogan. Thinnes played Roger Collins in the 1991 revival of TV's Dark Shadows. He also appeared on General Hospital as Phil Brewer from 1963 to 1966, on One Life to Live as Alex Crown from 1984 to 1985, and as Sloan Carpenter from 1992 to 1995. He also played a lead role in "The Crystal Scarab", a first season episode of Poltergeist: The Legacy in 1996.
As well, Thinnes made two appearances in "The X-Files" as Jeremiah Smith, an alien rebel with healing and shape-shifting abilities. His character initially appears in a two-part arc-narrative, the first of which closes Season Three ("Talitha Cumi" , and the second of which opens Season Four ("Herrenvolk"  ). Thinnes's second appearance was in Season Eight, Episode 14 ("This Is Not Happening" ).
Thinnes also appeared in the three-hour, 1995 TV mini-series The Invaders starring Scott Bakula, in which he returned as a much older David Vincent.
Thinnes twice appeared on the ABC soap opera One Life to Live playing two different characters. From 1984-1985, he played the role of "Alex Crown" and from 1992-1995, he played the role of "Gen. Sloan Carpenter." During both of his stints on the show, his characters became a father-in-law to the same character, "Cassie Callison" then died.