Darren Wilson, 28, had been on administrative leave since the August 9 shooting.
His resignation was announced on Saturday by one of his lawyers, Neil Bruntrager, the Associated Press news agency and local newspaper the St Louis Dispatch reported.
Bruntrager said the resignation was effective immediately.
"I, Darren Wilson, hereby resign my commission as a police officer with the City of Ferguson effective immediately," the Dispatch newspaper quoted Wison's resignation letter as saying on its website.
"I have been told that my continued employment may put the residents and police officers of the city of Ferguson at risk, which is a circumstance that I cannot allow."
A grand jury spent more than three months reviewing evidence in the case before this week declining to issue any charges against Wilson.
He told jurors that he feared for his life when Brown hit him and reached for his gun.
The US Justice Department is still conducting a civil rights investigation into the shooting and a separate probe of police department practices.
The shooting struck up a national debate about race and police power