Resham Chaudhary won the seat from Kailali in western Nepal by a landslide, securing more than double the votes of his closest rival, according to results from the election commission.
Chaudhary has been in hiding since 2015 when he was accused of masterminding an attack in which eight police officers and a toddler were killed.
“He is in our wanted list and we can arrest him even though he has been elected as a member of Parliament, if we find him,” said police spokesman Manoj Neupane.
Chaudhary was a key figure in violent protests that erupted in 2015 over a contentious new constitution.
Ethnic minority groups from across Nepal’s southern lowlands took to the streets demanding changes to the charter, which they say leaves them politically marginalized.
Around 50 people died in clashes between protesters and police that led to a blockade of the border with India and a crippling shortage of goods in landlocked Nepal.
Chaudhary has previously denied masterminding the attack on police, which he described as a “people’s uprising.”
But a parliamentary committee concluded the killings were premeditated, and a Human Rights Watch investigation found some protesters appeared to have come prepared for violence.
The protest movements have lost momentum in recent years and many of their leaders have joined political parties.
During his campaign, Chaudhary never once emerged from hiding. Instead he recorded a series of audio and video speeches that his supporters played on laptops at crowded rallies, according to local media.
This is not the first time a man on the police’s wanted list has ended up in Nepal’s Parliament.
Shortly after being elected to Parliament in 2013, Sanjay Sah was arrested for his role in a deadly bombing the year before. He is still in jail.
Votes are still being counted following landmark national and provincial elections, which mark the end of the country’s tumultuous transition from monarchy to democracy 11 years after the end of a brutal civil war.
Final results are expected by the end of the week, but an alliance of the two main communist parties has already won a strong majority.