Mr Kan has been criticised for failing to show leadership after the devastating 11 March earthquake and tsunami, and ensuing nuclear crisis.
In June, Mr Kan pledged to quit if parliament passed three key pieces of legislation, which it did on Friday.
The ruling Democratic Party of Japan will choose a new leader on Monday.
Mr Kan's successor as party head will almost certainly become Japan's next prime minister.
Challenges ahead
Mr Kan announced his decision to stand down at a DPJ meeting, which was broadcast to the nation. He is expected to give a news conference later on Friday.
Looking back on nearly 15 months in office, Mr Kan said he had done all he could given the difficulties he faced, including the Fukushima Daiichi nuclear disaster and political infighting - including within his own party.
"Under the severe circumstances, I feel I've done everything that I had to do," he said. "Now I would like to see you choose someone respectable as a new prime minister."
The 64-year-old's resignation had been widely expected, and comes amid tumbling public support.
On 2 June he won a no confidence vote in the Diet (parliament), only by making a promise to step down at a future date.
The Diet passed the final two bills out of three earlier on Friday - one on the budget, the other promoting renewable energy - which he had set as a condition for his departure.
The BBC's Roland Buerk in Tokyo says the new prime minister will have to oversee the biggest reconstruction effort in Japan since WWII and resolve the nuclear crisis at Fukushima where reactors are still leaking radiation.
They will also have to persuade the markets that Japan can overcome a divided parliament to address the biggest national debt in the industrialised world, our correspondent says.
Seiji Maehara, a hawk on China who argues for pursuing growth before raising taxes to restore the nation's fiscal health, is favourite among the public.
But the decision will be made by the governing party's Diet members.
Reports in Japan say Ichiro Ozawa, who leads the biggest faction despite the suspension of his party membership over a political funding scandal, is unlikely to support the former foreign minister.
Other possible successors include Finance Minister Yoshihiko Noda and Trade Minister Banri Kaieda.
Slow recovery
The twin natural disasters claimed more than 15,700 lives, and more than 4,500 people remain unaccounted for. Survivors in Japan's devastated north-east have complained about slow recovery efforts.
The resulting crisis at the Fukushima Daiichi plant is the world's worst nuclear accident in a generation.
Three of the six reactors melted down after the tsunami and 9.0-magnitude quake wrecked cooling systems.
The opposition and many in Mr Kan's own party said he failed to show leadership in the crisis, and was too slow in acknowledging the severity of the disaster.
The crisis also revealed serious flaws in the nuclear industry's regulatory systems and safety standards.
Workers are continuing to bring the plant to a cold shutdown by January.
However, nearly six months on many of the 80,000 people who were evacuated from the area are living in temporary housing or shelters, with no indication of when or if they will be able to return home.
The 64-year-old's resignation had been widely expected, and comes amid tumbling public support.
On 2 June he won a no confidence vote in the Diet (parliament), only by making a promise to step down at a future date.
The Diet passed the final two bills out of three earlier on Friday - one on the budget, the other promoting renewable energy - which he had set as a condition for his departure.
The BBC's Roland Buerk in Tokyo says the new prime minister will have to oversee the biggest reconstruction effort in Japan since WWII and resolve the nuclear crisis at Fukushima where reactors are still leaking radiation.
They will also have to persuade the markets that Japan can overcome a divided parliament to address the biggest national debt in the industrialised world, our correspondent says.
Seiji Maehara, a hawk on China who argues for pursuing growth before raising taxes to restore the nation's fiscal health, is favourite among the public.
But the decision will be made by the governing party's Diet members.
Reports in Japan say Ichiro Ozawa, who leads the biggest faction despite the suspension of his party membership over a political funding scandal, is unlikely to support the former foreign minister.
Other possible successors include Finance Minister Yoshihiko Noda and Trade Minister Banri Kaieda.
Slow recovery
The twin natural disasters claimed more than 15,700 lives, and more than 4,500 people remain unaccounted for. Survivors in Japan's devastated north-east have complained about slow recovery efforts.
The resulting crisis at the Fukushima Daiichi plant is the world's worst nuclear accident in a generation.
Three of the six reactors melted down after the tsunami and 9.0-magnitude quake wrecked cooling systems.
The opposition and many in Mr Kan's own party said he failed to show leadership in the crisis, and was too slow in acknowledging the severity of the disaster.
The crisis also revealed serious flaws in the nuclear industry's regulatory systems and safety standards.
Workers are continuing to bring the plant to a cold shutdown by January.
However, nearly six months on many of the 80,000 people who were evacuated from the area are living in temporary housing or shelters, with no indication of when or if they will be able to return home.
Source : BBC
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