The 66-year-old former Paris Saint-Germain and Brazil international centre-back on Wednesday said he made the decision after learning of the club's search for another manager, reports Xinhua news agency.
"I felt like I didn't have support and was isolated at times," Braga said in a statement that confirmed his departure.
"What I can say is that Flamengo are bigger than this. The club is going to flourish because of all the work that has been done in the last few years... and because of its greatness.
"I have always been prepared to deal with pressure and big moments and I always handled it well. I'm used to taking on big challenges with my head held high. But...I don't accept betrayal," he added.
Flamengo did not immediately comment on Braga's decision and it was unclear on Wednesday who would assume the vacant position.
The Rubro-Negro are currently sixth in Brazil's 20-team Serie A standings with three wins and a draw from six matches. They are also still alive in the Copa do Brasil and the Copa Libertadores, South America's top club competition.
Braga, who was capped once for Brazil's national team in 1978, had been in charge of Flamengo since January.
( With inputs from IANS )