The acting secretary general has been at the National Press Club since Monday amid brewing tensions over the first anniversary of the last general elections.
Police's Deputy Commissioner Masudur Rahman said Fakhrul had been arrested on specific charges.
He has been taken to the detective police's Minto Road office.
Fakhrul was picked up minutes after he had left the the press club on the first day of the opposition-sponsored nationwide transport blockade on Tuesday.
He is accused in over 50 cases. Paltan police said he had been implicated in two more cases filed on Monday over arson attacks in Dhaka.
Police locked the BNP's central office on Saturday night and had since kept party chief Khaleda Zia's Gulshan office surrounded.
Meanwhile, the party's Thakurgaon unit has called for an indefinite shutdown in Fakhrul's home district minutes after his arrest.
BNP supporters marched down the streets, vandalised vehicles and blocked the Dhaka-Thakurgaon road with logs and burning tyres. Border guards have been called out to assist police to patrol streets.
Fakhrul came to the press club on Monday to attend a programme of a BNP affiliate marking the polls anniversary.
The ruling party and BNP activists fought pitched battles later that day over his presence at the press club.
Awami League supporters surrounded Fakhrul's car and shouted slogans after he had got out Tuesday.
They had been observing a sit-in protest there led by the prime minister's Information Affairs Advisor Iqbal Sobhan Chowdhury.
Fakhrul addressed the media on Tuesday afternoon before trying to leave the place in his car.
Police appeared ready to arrest him outside the press club.
They stopped Fakhrul's car at the gate around 4pm and several policemen barged into it before driving it away to the detective police's office.
Deputy Commissioner Masudur Rahman told bdnews24.com that the BNP leader would be produced in court on Wednesday.
Khaleda has condemned Fakhrul's arrest and demanded his immediate release.
BNP leader Mirza Fakhrul arrested
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