"He's a different kind of a guy. He's got a lot of good ideas, but he's got a lot of ideas," Trump told reporters outside the White House.
Kennedy has come under increasing bipartisan criticism on Capitol Hill over his handling of vaccines and other issues.
Responding specifically to a decision in Florida to end all mandates on vaccines for children, Trump said over the weekend that "you have some vaccines that are so incredible. I think you have to be very careful when you say some people don't have to be vaccinated. It's a very tough position."
The president continued that "you have vaccines that work. They just pure and simple work. They're not controversial at all, and I think those vaccines should be used, otherwise some people are going to catch it, and they endanger other people. And when you don't have controversy at all, I think people should take it."
The president also defended Kennedy after he was subjected to tough questions at a Senate hearing on Thursday, saying that Kennedy's "got a different take, and we want to listen to all of those takes."
"But it's not your standard talk, I would say. And that has to do with medical and vaccines. But if you look at what's going on in the world with health, and look at this country also with regard to health, I like the fact that he's different."
Kennedy has repeatedly suggested a link exists between autism and vaccines, The Hill reported. He told Trump last week that HHS is on track to identify "interventions" that he claims are "certainly causing autism," along with possible ways to address them by September.