Members of Fallon's band The Roots are seen with instruments typically found in a classroom, while Thicke plays a pair of spoons.
Thicke's "Blurred Lines" (featuring T.I. and Pharrell) has spent spent eight weeks at the top of the Billboard charts. It scored extra attention after a Daily Beast writer homed in on the song's "I know you want it lyrics" and NSFW video as "kind of rapey."
Thicke took to NBC's "Today" show Tuesday and brushed off the controversy.
"When we made the song we had nothing but the most respect for women," he said, adding that he welcomed the "conversation."
"That's what great art does. It's supposed to stir conversation, it's supposed to make us talk about what's important," Thicke said.
Watch the cover of "Blurred Lines" on Fallon below:
And in case you missed them, check out earlier "Late Night" covers featuring kids' instruments with singers Mariah Carey and Carly Rae Jepsen.