The 38-year-old actor defended his relationship with the late singer as a "legitimate" connection during Tuesday's episode of the Inside of You with Michael Rosenbaum podcast.
Culkin said he had a genuine friendship with Jackson, who died at age 50 in June 2009, despite their 22-year age difference.
"I mean, at the end of the day, it's almost easy to try to say it was 'weird' or whatever, but it wasn't, because it made sense," the star said. "Like, we were legitimate."
"We were friends -- in the most simple kind of [way]," he added. "It's one of my friendships that people question, only because of the fact that he was the most famous person in the world."
Culkin was 10 years old when his starring role in the 1990 movie Home Alone catapulted him to fame. Jackson, who rose to stardom with the Jackson 5 as a child, could relate to Culkin's experience.
"He reached out to me because a lot of things were happening big and fast with me. And yes, I think he identified with that," the actor said of Jackson.
"He was the kind of person who had been through the exact same frickin' thing and wanted to make sure that I wasn't alone in that," he added. "He was hilarious, sweet. People didn't know how funny he [expletive] was."
Culkin testified on Jackson's behalf during the singer's child molestation trial in 2005, calling the accusations against the star "absolutely ridiculous." He remains friends with Jackson's children, including the singer's 20-year-old daughter, Paris Jackson, who recently entered treatment for her emotional health.