Krstajic came under fire after Serbia made a group-stage exit in the 2018 World Cup and despite winning their pool in the Nations League Group C, pressure intensified after they suffered a 5-0 mauling by Ukraine in Euro 2020 qualifying on Friday.
Krstajic appeared to have gained breathing space after a 4-1 win over Lithuania on Monday, but fans, pundits and media remained relentless in their criticism of the former international defender and his tactics.
"The FSS executive board and coach Mladen Krstajic have terminated cooperation by mutual consent and a decision will be made in the forthcoming period who will take over," the FSS said on its official website.
"We thank Krstajic for his efforts and especially on his Nations League accomplishments. We wish him all the best in his future endeavours."
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Serbia are third in Euro 2020 qualifying Group B with four points from three games, behind Luxembourg on goal difference and six adrift of leaders Ukraine.
They are at home to European champions Portugal on Sept. 7 and away to Luxembourg three days later in their next two qualifiers, with local media reporting that former Montenegro coach Ljubisa Tumbakovic is the prime candidate to take over.
Tumbakovic, a 66-year old Serb, was fired by Montenegro after he boycotted Friday's Group A qualifier against Kosovo, with the Adriatic nation's media reporting that he came under pressure from Serbian fans to pull out of the fixture.
Serbia's former southern province Kosovo, whose population is more than 90 percent ethnic Albanian, has been recognised as a sovereign state by more than 110 countries since it declared independence from Serbia in 2008.
A group of nations, including Serbia, China, five EU members and Russia, refuse to recognise it.
(Reporting by Zoran Milosavljevic; Editing by Ed Osmond)
