Lead singer Tim Burgess tweeted that the band was "torn apart" by Brookes' death.
"Jon Brookes, my friend, our drummer and inspiration to so many, passed away this morning. We are torn apart. Love & thoughts to Jon's family," he said.
Brookes was diagnosed with a brain tumor in 2010 after collapsing onstage during a concert in Philadelphia. He had been working on new material with The Charlatans this summer.
Brookes was a founding member of the band, which drew on funk, rock and psychedelia and came to be associated with the early 1990s "Madchester" scene. The Charlatans' multiple British hits include "The Only One I Know" and "Can't Get Out of Bed."
In the United States, the band added "UK" to its name because there had already been an influential group in the late 1960s called The Charlatans. In the U.S. the band has scored four top 20 hits on what is now known as Billboard's Alternative Songs chart, with 1992's dance-friendly "Weirdo" being their lone number one.
He is survived by his wife and three daughters.