In an interview, the tennis legend was asked why Williams, who is expecting her first child, was the best female tennis player but not the best player in the world in his view.
McEnroe went on to say that while the 23-time Grand Slam winner was an "incredible" player, she would rank "like 700 in the world" if she played against male competitors.
"If she played the men's circuit she'd be like 700 in the world," McEnroe said. "That doesn't mean I don't think Serena is an incredible player."
"I do, but the reality of what would happen would be I think something that perhaps it'd be a little higher, perhaps it'd be a little lower."
The remarks brought about a lot of debate and discussion as well as controversy as many felt McEnroe's comments were unnecessary with Williams taking to Twitter to respond to the former three-time Wimbledon champion.
"Dear John, I adore and respect you but please please keep me out of your statements that are not factually based," Williams wrote on Twitter.
"I've never played anyone ranked "there" nor do I have time. Respect me and my privacy as I'm trying to have a baby. Good day sir."
McEnroe has now come out to claim that while he did not mean to undermine Williams, he still stands by his comments.
"She's the greatest female player that ever lived," the 58-year-old told CBS, as quoted on SportingNews.
"Then the lady said to me, I don't remember which one, but she said, 'why did you say woman, why don't you just say the greatest, you know, tennis player that ever lived' and so then I felt the need, however unfortunately probably, to defend myself. I don't know, just say what I really felt, which is about what I think she would be.
"I don't want anything to go wrong with Serena because she's pregnant. I don't want to upset her or whatever it was. She's — I think she was doing a tongue-in-cheek as well. And I think that deep down we're talking about something — I can't even believe we're talking about it."
McEnroe went on to poke fun at the whole outrage by re-ranking his top five tennis players of all time, including Williams at number five.