The verdict comes as tensions remain high in the semi-autonomous city with fears growing that Beijing is tightening its grip.
Wong was convicted for taking part in an unlawful assembly after he and other students climbed into a Hong Kong government complex forecourt known as Civic Square on September 26, 2014.
That protest triggered wider rallies that exploded two days later when police fired tear gas to disperse crowds.
The verdict could see Wong jailed for up to five years.
Fellow student leaders Alex Chow and Nathan Law were also convicted over the same protest Thursday - Chow for taking part and Law for inciting others to do so.
"No matter what is the penalty... we will still continue to fight against suppression from the government," Wong said after the ruling.
"We know facing the largest communist regime in the world is a long-term battle for us to fight for democracy."
The three defendants, who smiled in resignation at the verdict, were released on bail and are due back on court on August 15 for sentencing.
Interference by Beijing
Teenage Wong, now 19, was at the forefront of the "Umbrella Movement" which brought parts of the semi-autonomous city to a standstill for more than two months in 2014 as residents called on Beijing to allow fully free elections of future leaders.
Young campaigners were left angry and frustrated after the rallies failed to win political reform from Beijing, with Wong and Law since founding a new political party, Demosisto, campaigning for self-determination for Hong Kong.
Pro-independence groups demanding a complete split from Beijing have also emerged.
File image of student activist Joshua Wong leading protests in 2015 Source: AAP
Wong has been in and out of court hearings for the past year after being charged with multiple offences linked to various protest actions.
In the ruling Thursday, magistrate June Cheung said Wong had known that climbing over the fence may "disturb order".
Defence lawyers had argued that authorities should not have fenced off Civic Square - previously a popular protest site open to the public - in the febrile months before the Umbrella Movement.
The prosecution said the fact they climbed into the square was unlawful and that the protest was pre-planned.
Both Wong and Law were acquitted in June over an anti-China protest in the first of a series of cases against him to reach a verdict.
Another student leader, Billy Fung, was charged Thursday over a protest in January where students stormed into an official meeting at Hong Kong University angered by the appointment of a pro-Beijing figure to a senior university role.
There is concern that Beijing is increasingly interfering in education and media, as well as politics.
Hong Kong was returned to China by Britain in 1997 with its freedoms guaranteed for 50 years, but there are fears those liberties are disappearing.
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