The man who leads the protests accusing the Pakistani army of violating human rights was arrested for alleged conspiracy and criminal sedition.
Manzoor Pashteen was arrested in Peshawar, along with nine others from his Pashtun Protection Movement.
Pashteen attracted tens of thousands to rallies in cities around Pakistan.
A fellow protest leader said he was being punished for simply demanding human rights. The powerful military, unaccustomed to criticism, denies wrongdoing.
Pashteen, a charismatic former veterinary student who gained prominence two years ago, became the face of the Pashtun Tahaffuz (Protection) Movement (PTM), in a country where few openly challenge the military.
A number of cases highlighted by the PTM and investigated independently by the BBC came to light in a report from last year.
"It took us almost 15 years of suffering and humiliation to muster up the courage to speak up and publicize how the military trampled on our constitutional rights through direct action and policy in support of militants," Manzoor Pashteen told the BBC. .
The non-violent protests started with the alleged extrajudicial killing of a young man of Pashtun ethnic origin by the police in Karachi.
The movement then expanded, demanding responsibility from the Pakistani army for alleged human rights abuses against Pashtuns during the war against Islamic extremists in the northwest of the country.
Pashtuns make up the majority of the population along the border with Afghanistan. The protests, which sometimes drew tens of thousands of protesters, shook the military.
A protest that threatens the power of the army
By Abid Hussain, BBC Urdu in Islamabad
Since January 2018, Manzoor Pashteen and his movement have become the most significant challenge for the military.
Historically, in Pakistan, such movements have often failed or been co-opted by the state – but the PTM has grown and grown in strength. Meanwhile, his 27-year-old leader, with his trademark red cap, firmly maintains a modest lifestyle – he doesn't even have security details to speak of.
The state does not seem sure how to act against him, and the decision to arrest him seemed to be sudden. The charges were filed on January 21, but it took a week to make the arrest.
Almost laughing, the reason cited for the change is that he speaks offensively about Pakistan and refuses to accept the constitution, when he often emphasizes in his speeches the need to defend the law.
Now that the state has finally made its move, how will the PTM respond? Manzoor Pashteen assured that, while leading the movement, no violence occurred. But will your supporters now show the same discipline?
Manzoor Pashteen was accused of "hate speech" and sedition, among other crimes. The latter has a possible life sentence.
He was held in police custody in Peshawar for 14 days, but is expected to appear before a magistrate in Dera Ismail Khan, some 300 km south, where charges were brought against him.
His fellow protesters demanded his immediate release. Another PTM leader, MP Mohsin Dawar, urged supporters to remain calm in response to the arrest.
This is the first time that Manzoor Pashteen has been arrested, and why the authorities chose to detain him now is unclear.
Authorities have repeatedly arrested other PTM leaders and activists since the movement gained prominence. Last year, Mohsin Dawar and his PTM colleague at the National Assembly, Ali Wazir, were detained for four months after a deadly confrontation in Waziristan.
A media blackout ensured that PTM's peaceful rallies were left out of the front pages and on TV newsletters – although the movement was successful in getting its message out on social media.
According to authorities and independent research groups, militant violence since 2002 has forced more than five million people in northwest Pakistan to leave their homes in search of refuge in government-run refugee camps or in rented houses in peaceful areas.
There are no official figures for the total death toll in this war, but estimates by academics, local officials and activists indicate that the number of civilians, militants and security forces killed at more than 50,000.
Many see the PTM as an innovator in the political landscape of a country where proxy wars have deprived large populations not only in tribal areas and in the northwest, but also in Balochistan and other parts of the country.