The man, identified as Abu Talha, was accused of being the chief "coordinator" of a "cell that prepared a string of explosions in Lebanon" including in Beirut's Burj al-Barajneh district, the security source said.
He was seized in a special operation carried out by an elite unit of the Internal Security Forces (ISF) in the northern port city of Tripoli, the source told AFP.
The explosions in the densely populated neighbourhood of Burj al-Barajneh on November 12 killed 44 people. They were claimed by the Islamic State jihadist group.
Security forces had been monitoring Abu Talha for "a long period," including when he went into hiding after the December arrest of Bilal al-Baqqar, another prominent planner, the source added.
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In an emailed statement, the ISF confirmed it had arrested Abu Talha in a dawn raid on a residential building in Tripoli.
It said he was being interrogated.
A security source in northern Lebanon said Abu Talha, born in 1986, was also known as Khaled Seifeddine Zeineddine.
At the time, he said "the whole suicide bombing network" behind the Burj al-Barajneh blasts had been arrested.
Tripoli is one of Lebanon's most volatile cities, and fighting has broken out there between its majority-Sunni population and minority of Alawites, an offshoot of Shiite Islam.