Lithgow appeared in two episodes of the latest season as the estranged father of Barney (Neil Patrick Harris).
Thomas has now revealed that he would like Lithgow to come back in future episodes.
"We absolutely want to see John Lithgow again," he told TV Line. "We're hoping to bring [him] back."
Thomas also explained that he would like Six Feet Under star Frances Conroy to reprise her role as Barney's mother Loretta.
"I know John Lithgow specifically would love to work with her," he said.
How I Met Your Mother, which has been renewed for two more seasons, will return with new episodes on CBS in the fall.
Watch a clip of John Lithgow starring in How I Met Your Mother below: