Andrew Lipovsky/NBC
"Have you seen my show? I'm never too hard on anyone," Fallon told TMZ in a video interview.
The "Tonight Show" host's playful, softball interview, which ended with his toughest question - whether Trump would let him mess up the candidate's hair - inspired a lot of heated criticism among viewers and members of the media.
Huffington Post writer Maxwell Strachan called the interview "an extended on-air puff piece" and dinged Fallon for playing nice with a controversial figure running for the highest job in the nation.
Meanwhile, viewers took to social media to berate Fallon's performance. Their comments included calling the interview "sickening" and making comparisons of the interview to Nazi propaganda.
I can't make any jokes about Jimmy Fallon. The way he showcased Trump like a lovable old grandpa was sickening.
Next up: Fallon and Trump slow jam MEIN KAMPF. Hilarious!
- Harold Itzkowitz (@HaroldItz) September 16, 2016
As for Trump allowing the host to mess up his hair, Fallon said Trump didn't know he was going to ask until two minutes before it happened.
"We always ask everybody before we do everything," Fallon said. "I'm not one of those gotcha people."
Hillary Clinton will have her turn on NBC's "Tonight Show" on Monday.
"We'll do something fun with her too," Fallon said.
Watch the video interview below: