Han Sang-Gyun, the head of the Korean Confederation of Trade Unions (KCTU), was charged with inciting violence and obstructing justice during a massive anti-government rally in November, Yonhap news agency said.
Dozens of police officers and protestors were injured and dozens of police buses damaged in the November 16 protest in central Seoul.
To evade arrest following the rally, Han sought sanctuary in the capital's Jogye Temple, where leading monks negotiated with police over his fate.
Tensions had run high around the temple, with hundreds of police facing off against a human barricade of monks and lay Buddhists.
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South Korean religious venues have a long history of providing refuge for political activists, most notably in the 1980s when many pro-democracy activists sought sanctuary from police arrest in Catholic churches.
The November protest -- involving more than 60,000 people -- was the largest in more than seven years in the South.
Protestors demanded that Seoul scrap labour reforms that critics say would make it easier for firms to fire workers.