Lauper, 66, and Clarkson, 37, delivered a stripped-down but powerful rendition of the 1986 song, with Lauper also playing the dulcimer.
Clarkson said it was a "dream come true" to perform the song with Lauper. "True Colors," written by Billy Steinberg and Tom Kelly, was the title track on Lauper's album of the same name.
Prior to the duet, Lauper and Clarkson discussed Lauper's rock and roll sense of style. Lauper said she doesn't foresee herself ever dressing more conservatively.
"I just don't want to feel like I look in the mirror and I look conservative and straight," the star said. "Sometimes I pass Brooks Brothers and I think to myself, 'Well, that ain't bad.' What do you mean, that's bad!"
"I don't know what older artists look like," she added before telling Clarkson, "What I always think of is your song 'What Doesn't Kill Me.' Whenever I was feeling really kind of downtrodden, I would sing along with [it]."
Lauper last released the album Detour in May 2016. As an actress, she guest starred as Avalon Harmonia on Bones in 2017 and as Vanessa Nero on Magnum P.I. the next year.