Rao Shakir, a suspected member of banned militant group Lashkar-e-Jhangvi, was arrested from Bhara Kahu on the outskirts of the federal capital late on Friday night, the police said.
The militant is believed by the police to be closely linked to the Al-Qaeda and Taliban groups and their commanders.
Pearl was abducted from Karachi in 2002 while doing a story on militant funding. His remains were later found in a grave on outskirts of the port city.
Shakir is also linked to several terrorist strikes, including a suicide attack on a bus of a spy agency, the suicide bombing of the Marriott Hotel last year and an attack in Rawalpindi.
Officials said police had been hunting for Shakir for a long time. A police spokesman said his accomplices were arrested earlier. The arrested man also allegedly provided safe houses to militants.
Shakir's arrest comes as Pakistani military in continued operations maintained its pressure on the Taliban in the restive north west region killing two and capturing six other militants.