Kolin said Flint, 57, chief since 2004, will receive six months' severance pay and up to $7,000 in reimbursement for legal expenses.
Kolin said he could not discuss why Flint is resigning because it is a personnel matter.
The Santa Rosa Police Department has been involved in a controversy that resulted in the firing in May of Capt. Jamie Mitchell, the department's second-in-command.
Mitchell and Flint are the targets of complaints alleging they retaliated against employees who complained about dysfunction within the police department. Mitchell has sued the city, claiming he was fired to placate those employees. His suit is in federal District Court in San Francisco.
Kolin praised Flint's "commitment and contribution to the community." He said the city's crime rate has decreased and that the department's traffic safety and enforcement and gang intervention programs have been recognized in California and nationwide.
The city will interview retired police chiefs outside the area to find an interim chief and then will conduct a statewide search for about six months to find a new police chief, Kolin said.
"The city wishes Chief Flint well and looks forward to a smooth transition of leadership in the Department," Kolin said.