Last year, Mr. Trump accused Islamabad of "nothing but lies & deceit, thinking of our leaders as fools", and suspended $300 million in military aid to the Pakistani government.
His two charities were banned in February previous year, and the government froze their assets in compliance with a United Nations request.
The U.S. has labelled Saeed a Specially Designated Global Terrorist, and since 2012 has offered a $10 million reward for information that helps bring him to justice.
Sources within the CTD said the JuD chief was taken into custody when he was traveling to Gujranwala from Lahore.
The arrest came days before a visit to Washington by Prime Minister Imran Khan, who has vowed to crack down on militant groups operating in Pakistan.
The tweet refers to a "10-year search" although Saeed's whereabouts were known to the authorities in Pakistan.
Mr Saeed founded Pakistan's Lashkar-e-Taiba (LeT) group, which has been banned since 2002.
Saeed's arrest comes at a time when Pakistan has been under increasing pressure to crack down on militant groups.
Since the Khan government has taken control of the JuD and the FIF properties including seminaries and mosques across the country following worldwide pressure built up after the deadly Pulwama attack, Saeed was keeping a low profile at his Lahore's Jauhar Town residence. The watchdog gave Pakistan an October deadline to improve its efforts against terror financing.
Born in 1948, Hafiz Saeed along with his family started migrating from East Punjab and reached Pakistan in around four months in the autumn of 1947.
Another security official said the arrest relates to terror financing charges.
Reportedly, Saeed was travelling from Lahore to Gujranwala when the arrest took place. Pakistan said Saeed had been cleared by its courts and sought more eveidence from India.
Previously, Mr Saeed had been detained several times, along with some of his close aides, but had not been charged or put on trial.
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