Michel Djotodia made the announcement at a regional summit in Chad aimed at ending violence that has engulfed the country.
CAR’s entire transitional assembly is attending the meeting in Chad organised by regional leaders.
Michel Djotodia, CAR’s first Muslim leader, had been resisting pressure to go.
His seizure of power last year has led to 20% of the population fleeing their homes amid fighting between Christian and Muslim militias.
The UN has warned of an impending humanitarian disaster.
Since December and the arrival of more regional peacekeepers and French troops, 1,000 people have died in sectarian clashes.
Many villages are deserted and in the last month the number of those who have fled their homes has doubled – including almost half of those living in the capital city, Bangui.
Michel Djotodia’s resignation was made in a statement by the 10-nation Economic Community of Central African States (ECCAS).
CAR PM Nicolas Tiengaye, with whom he had a fractious relationship, has also resigned, the AFP news agency reports.
Earlier ECCAS Secretary-General Ahmat Allami said members of CAR’s National Transitional Council (CNT) had been flown in at short notice to decide the leadership of their nation.
The lawmakers met regional leaders while Michel Djotodia held separate talks with allies from his former Seleka rebel alliance, AFP reported.
Under a deal brokered by regional powers last year, the CNT was charged with choosing a transitional leader to take CAR to elections due at the end of 2014. It formally elected Michel Djotodia to his position as interim president last April.
Earlier on Friday, thousands of people in Bangui took to the streets demanding the resignation of Michel Djotodia, a former Soviet-trained civil servant.
Seleka seized power last March overthrowing the then-President Francois Bozize, from CAR’s majority Christian population.
Although Michel Djotodia officially disbanded the Seleka rebels, he has proved unable to keep them in check.
Their actions have prompted Christians to form vigilante groups, sparking a deadly cycle of revenge attacks.
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