Bolsonaro will be hospitalized for one to two days in Sao Paulo for the procedure, newspaper Estado de S.Paulo said, citing unnamed medical and presidential palace sources.
The president's office did not immediately respond to a request for comment. His press office told Estado and newspaper Folha de S.Paulo that "there are no details on the matter yet."
Bolsonaro said in late August that he would undergo a procedure to remove a kidney stone this month, although he later said it was actually a bladder stone.
"I have had it more than five years. It's in the bladder, bigger than a bean. I resolved to take it out, as it is probably hurting the inside of the bladder," he told supporters outside his residence on Sept. 1.
Bolsonaro's health has been a concern since he was stabbed while on the campaign trail in 2018, and he subsequently underwent several surgeries.