The announcement followed a string of decisions that recently have rolled back Mutko's formal involvement in Russian sport as the country faced additional scrutiny over its doping scandal and its role as World Cup host.
The Russian Football Union will elect a new president on Feb. 22 and Sergei Pryadkin, vice president of the Russian Football Union and president of Russia's Premier League, will serve as head of the union until then, executive committee member Igor Lebedev wrote on Twitter.
"As president of the Russian Football Union, I was faced with the task of normalising Russian soccer, and then with a new challenge - the World Cup," Mutko told TASS news agency. "Overall these tasks have been fulfilled. I'm satisfied with the results of my work."
Mutko did not explain his resignation in any detail, saying only that "the time has come to elect a new president."
Mutko, who oversaw sport at the height of Russia's doping scandal, had temporarily stepped down from his role as president of Russia's Football Union last year after the International Olympic Committee (IOC) banned him from the Olympics over allegations of state-sponsored doping at the 2014 Sochi Games.
Russia has denied the allegations, and Mutko has appealed the IOC's decision at the Court of Arbitration for Sport (CAS).
CAS has yet to set a hearing date.
Mutko served as Russia's sports minister from 2008 to 2016 and was then put in charge of sport as deputy prime minister. In May, just a month before the World Cup opener, he was made a deputy prime minister overseeing construction.
Mutko also stepped down as head of Russia's World Cup Local Organising Committee six months before the tournament.
President Vladimir Putin has staunchly defended Mutko, saying that it had been impossible to dismiss him after he became the target of unfair attacks related to the doping scandal.
Despite phasing out his formal involvement in Russian sport, Mutko has remained close to the field.
He attended World Cup matches, regularly dropped in on the Russian national team and met with former FIFA president Sepp Blatter in Moscow during the tournament.
When asked by Reuters in what capacity he was attending a Russia training session during the World Cup in June, Mutko said: "In the capacity of a person."
(Reporting by Gabrielle Tétrault-Farber; Editing by Martyn Herman)
