Brookes suffered a seizure while on tour with the group in Philadelphia three years ago. Diagnosed with a brain tumor, he underwent several operations, but had been working on new material with the band this summer.
The musician "passed away peacefully in hospital early this morning with his family at his bedside," the band said on in an online message Tuesday.
The exact cause and location of his death were not immediately disclosed.
"Jon was 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. Losing someone who was always so full of life is a tragedy that will be shared by so many. Our thoughts are with Debbie and all of Jon's family," the band said in a statement.