"Dear John, I adore and respect you, but please, please keep me out of your statements that are not factually based," she tweeted.
Williams, 35, continued, "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."
Williams comments were in response to an interview the former tennis star gave to NPR, saying that if Williams played "the men's circuit, she'd be like 700 in the world."
McEnroe's comments came after the NPR reporter had said of Williams, "She's the best player in the world."
"Oh! Uh, she's not, you mean, the best player in the world, period?" McEnroe responded.
For his part, McEnroe told CBS This Morning that he now puts Williams at number five in the all-time rankings.
Although McEnroe said earlier that he wouldn't apologize and that he was just calling it "like it is," the 58-year-old did wish Williams well.
"Serena, have a great time with the baby," he said.
McEnroe added, "I respect Serena very much so ... she's the greatest female player that ever lived."