Joshua Wong, Nathan Law and Alex Chow are accused of climbing a fence to break into a government compound at the start of the demonstrations.
Mr Wong, 18, has said he did not do anything illegal.
The protests, against proposed changes to Hong Kong electoral system, began in late September.
At the height of the movement, tens of thousands of people were occupying major streets demanding fully free elections for the territory's next leader, after Beijing said it would vet potential candidates.
The three students were among a large group of people who stormed the fenced-off Civic Square inside a government compound on 26 September, as an act of protest.
Images of the students being forcibly removed from the square by police, and other subsequent allegations of abuse of force by police, invigorated the protest movement.
Mr Chow has now been charged with taking part in an illegal assembly and Mr Law with inciting others to take part, while Mr Wong, leader of the Scholarism movement, faces both charges.
Mr Wong could be jailed for up to five years, but said he would not regret his actions and that it was a "political prosecution".
He said the break-in was "the best decision I have made within the four years I have been involved in the social movement and student movement".
Mr Wong's lawyer, Michael Vidler, said charging the trio so long after the event was "totally flawed" and a "clear abuse of process", AFP news agency reports.
Mr Wong and Mr Law are already facing charges of obstructing police officers.

Bicycles were wheeled down Whitehall to the Treasury by campaigners calling for increased government spending to protect cyclists and pedestrians.
Five people - three cyclists and two pedestrians - died on London's streets in the past week.
The Department for Transport said it was committed to reducing the number of deaths and casualties among cyclists.
Nine cyclists died in London in 2016.
Protesters have also been calling for a reduction in London's air pollution.
In front of the Treasury, campaigners laid down their bikes and dropped on to the wet pavement for a minute's silence.
Co-founder of campaign group Stop Killing Cyclists Donnachadh McCarthy said: "We have had enough of the breadcrumbs - we need real spending.
"We have had two tiny superhighways built, but they have been a huge success.
"They are the germs of a revolution which should spread all across London."
The campaigners want the chancellor to increase ring-fenced infrastructure expenditure on cycling and walking to 10% of the transport budget.
Many attending the demonstration also wore gas masks in protest at the worsening air pollution.
One sign read: "We are all canaries in London's toxic air."
Ben Wales, 32, died after colliding with a tipper truck in North Woolwich Road, Silvertown, east London, on Thursday afternoon.
Anita Szucs, 30, died after an apparent hit-and-run on Bounces Road, Enfield, on Monday while architect Karla Roman, 32, was killed in a crash with a coach on Whitechapel High Street, Tower Hamlets, on the same day.
A Department for Transport spokesman said: "Britain has some of the safest roads in the world but we are committed to reducing the number of cyclists killed and seriously injured."
They said that on top of a THINK! campaign to improve cycle safety they were spending "Â£300m on cycling funding in this Parliament" and more than Â£7bn improving road surfaces.
Three prominent Hong Kong student leaders have been charged over their roles in the pro-democracy "Umbrella Movement" of 2014.
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Hundreds of cyclists have staged a "die-in" protest in central London to raise concerns about road safety.