Dieudonne Kombo Yaya handed in his resignation on Friday, the National Elections Authority (ANE) told AFP in Bangui.
The ANE chief cited "pressure from CAR's presidency and the international community" over the election timetable for his decision to quit.
After twice postponing the elections the transitional authorities scheduled the first round of the presidential and legislative polls for October 18.
But many fear the security situation is still too turbulent for a peaceful vote.
According to a source in the presidency, a strategic committee has been formed to work out a new electoral calendar.
The Central African Republic has seen a recent upsurge in sectarian attacks, two years after a wave of bloodletting between Muslim fighters and Christian militias.
The government said Monday more than 60 people were killed in clashes in the capital last month, which it claimed were part of an attempted coup.
The violence raised fears of a return to the fierce violence unleashed by the 2013 ousting of then president Francois Bozize, a Christian, by mainly Muslim Seleka rebels.
UN rights investigators said earlier this year that estimates of between 3,000 and 6,000 killed in that bout of fighting failed to capture "the full magnitude of the killing".
One in 10 Central Africans -- 460,000 people -- have fled the country since 2013.