Wong and activist lawmaker Leung Kwok-hung, who RTHK radio said was also banned from Mong Kok, were charged with obstructing court bailiffs and did not enter a plea.
They are due to appear again in court on Jan. 14.
Wong, Leung and Lester Shum were among more than 100 people arrested in Mong Kok over the past two days. Wong's student group Scholarism confirmed the court ban.
The protesters are demanding open nominations for the city's next chief executive nomination in 2017. Beijing said in August it would allow a vote, but only among pre-screened candidates.
Lined with banks, noodle shops and gritty tenements, the streets of Mong Kok have been a key battleground for protesters and mobs intent on disbanding them, and was viewed as the protest site most likely to resist clearance.
While the protesters re-grouped and tried to storm back onto the roads, they ultimately failed to penetrate the mass of police armed with pepper spray and batons deployed to defend the major traffic intersections. Some protesters were hospitalised with head injuries from police batons.
The Mong Kok clearance was the second time in as many weeks that police, court bailiffs and workers moved to enforce court-ordered injunctions to clear the streets. The removal of the protesters' barricades, tents and furniture is a major blow to the movement which has been trying to wrest greater political freedom from Beijing.
The main protest site in Admiralty next to the city's chief executive office and barracks for China's People's Liberation Army remains largely intact. There is also a small protest site in the Causeway Bay shopping district.
Hong Kong, a former British colony, returned to Chinese Communist Party rule in 1997 under a "one country, two systems" formula that gave it some autonomy from the mainland and an undated promise of universal suffrage. — Reuters
