The 44-year-old passed away in hospital on Tuesday morning, surrounded by his family.
"Jon Brookes, my friend, our drummer and inspiration to so many, passed away this morning. We are torn apart," Charlatans frontman Tim Burgess said on Twitter.
"Love and thoughts to Jon's family."
Losing someone who was always so full of life is a tragedy that will be shared by so many.
The drummer was first diagnosed with a brain tumour after he collapsed on stage in Philadelphia in 2010. He had since been receiving treatment and had undergone a number of operations.
"He had been working on new material with the band over the summer," a further statement from the Charlatans said.
They hailed the musician, who is survived by his wife Debbie and three daughters, as "a brilliant drummer, an inspiration, a founding member of The Charlatans, part of our family and a friend to everyone in and around the band".
Jon Brookes' death is not the first tragedy to hit the band, as fellow founding member and keyboard player Rob Collins died in a road traffic collision in 1996.
The Charlatans released their debut single Indian Rope in 1990 and have since had more than 20 top 40 hits.