Kelly tore into Lemon, who she said "sees racism everywhere," as she alleged he gave "Chris Cuomo a total pass."
Cuomo and Lemon appeared to be sharing a joke – but many critics, including Kelly, did not find the comment funny.
"Weird how Don Lemon, who sees racism everywhere if a Republican is involved, gives his buddy a total pass on this," Kelly tweeted.
Alongside her post was a link to a New York Post article titled: "CNN host Chris Cuomo gets ripped for joking he is 'black on the inside'."
The 50-year-old host's controversial words followed his singing of the words to '70s sitcom Good Times - a show featuring an African American family.
Cuomo's rendition of the song prompted Lemon to laughed asked: "How do you know all the words to Good Times?"
The CNN host then responded with the highly criticized phrase: "You know I'm black on the inside."
Others slammed into Cuomo over the remark.
Journalist Aisha Staggers wrote: "Black is not a costume, I don't get to be white when I don't feel like not dealing with racism or racist police or just regular bulls**t black people deal with.
"I can't even hide at home because I can be killed there in my bed, so understand, there was nothing silly about this."
She added: "Black isn't something you can just say you feel you are inside without having to deal with the racism that comes wi
"We had to turn off the television because I’m not here for that nonsense. @CNN needs to have some sensitivity training with their on-air personalities" another person tweeted.
Some social media users likened Cuomo to his governor brother who is facing multiple allegations of sexual harassment - and has denied the claims.
Kelly and Cuomo have previously had riffs on Twitter.
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She tweeted about his battle with Covid, and slammed his brother, New York Governor Andrew Cuomo.
Kelly then told Page Six of Chris Cuomo: "The chief nurse assisting CNN’s suicide during the Trump era [is] now lecturing on how to cover news."