Huge crowds have taken to the streets recently — both against and in support of the former law professor — following his appointment by liberal President Moon Jae-in.
Cho’s relatives have been at the centre of probes involving educational privileges allegedly granted to his children, and also investments in an equity fund suspected of dubious operations.
Cho’s wife Chung Kyung-sim, a university professor, has been indicted for allegedly forging a college award for their daughter, with a trial slated to begin on Friday.
His two children have also been questioned by prosecutors.
Supporters say Cho’s family has been unfairly targeted by prosecutors because of his promise to reform the investigative agency.
“I have endured day after day trying to fulfil my duty to reform the prosecution,” Cho said in a statement, noting his “heavy heart”.
President Moon accepted Cho’s resignation and said he was “sorry for division” his appointment had caused.
But he noted Cho had dutifully carried out his mission during his 35-day stint and stressed the importance of following up on Cho’s unfinished work.
“His whole-hearted reform drive… has sparked consensus on its needs,” he said.
Education is South Korea is intensely competitive and top schools are frequently criticised for elitism — including by Cho, who said they create an “unfair society”.
He was accused of hypocrisy when it emerged he had sent his daughter to an elite institution, and that she had appeared to have benefitted from family connections.
Analysts say the scandal has laid bare worsening class divisions in South Korea, the world’s 11th largest economy.
Cho made a note of this Monday, saying he was “deeply sorry” for disappointing young people.