"Well look, North Carolina did something that was very strong, and they're paying a big price, and there's a lot of problems," Trump said on NBC's Today show, referencing the economic boycott against the state.
"You leave it the way it is," he added. "There have been very few complaints the way it is. People go, they use the bathroom that they feel is appropriate. There has been so little trouble, and the problem with what happened in North Carolina is the strife and the economic punishment that they're taking. So I would say that's probably the best way."
Host Matt Lauer then asked Trump: "If Caitlyn Jenner were to walk into Trump Tower, and wanted to use the bathroom, you would be fine with her using any bathroom she chooses?"
"That is correct," Trump replied.
Jenner, 66, a lifelong Republican, previously said she supports Trump and thinks he would be "good for women's issues."
Republican hopeful John Kasich has also voiced his opposition to North Carolina's new bathroom bill, while Ted Cruz has said he supports the measure.