Frere-Jones debuted as The New Yorker’s pop critic on March 8, 2004 with “Let’s Go Swimming” an essay on Arthur Russell. He followed in the footsteps of the magazine's past critics Ellen Willis, Mark Moses, Elizabeth Wurtzel, and Nick Hornby. He has covered lesser-known acts like Arcade Fire, Joanna Newsom, Grizzly Bear, Manu Chao, and Bon Iver, as well as established successes like Neil Diamond, Mariah Carey, Wu-Tang Clan, Lil Wayne, and Prince. Three essays originally published in the magazine have appeared in Da Capo's Best Music Writing anthologies. On October 22, 2007, The New Yorker published “A Paler Shade of White”, an essay in which Frere-Jones examined the changing role of race in pop, specifically indie rock and hip-hop of the last two decades. The piece proved to be controversial, eliciting responses from Playboy, The Village Voice, Slate, and Simon Reynolds, among dozens of other news outlets and blogs. The New Yorker received more mail about “A Paler Shade of White” than it did for any other essay since “Escaping Picasso,”Adam Gopnik’s December 16, 1996 essay about Pablo Picasso. Frere-Jones also appears in the 2009 documentary Strange Powers, by Kerthy Fix and Gail O'Hara, about Stephin Merritt and his band, the Magnetic Fields, in which he further discusses his ideas of race in pop music.
In 2008, Frere-Jones was named one of the top 30 critics in the world by Intelligent Life, the lifestyle publication from The Economist.
On March 9, 2009, The New Yorker published his first profile, of British pop singer Lily Allen.
At the end of 2009, he helped bring mainstream attention to then-unsigned indie rock band Sleigh Bells when he wrote that "After shows at Le Poisson Rouge and Public Assembly, I knew they were my favorite band in New York."
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