Hisham Al-Saedni, also known as Abu Al-Waleed Al-Maqdissi, was freed late on Thursday, the source said. Hamas declined immediate comment.
Saedni, in his late 50s, is believed to head the Jihadist Salafi group Tawhid and Jihad (One God and Holy War). The group adopts an Islamist ideology shared by al-Qaida, and sources said that Saedni himself joined al-Qaida in Iraq at the beginning of the US-led invasion in 2003.
Hamas had accused Saedni of attempting to disrupt public order in the Gaza Strip and arrested him on March 4, 2011.
Members identifying themselves with Tawhid and Jihad kidnapped and killed a pro-Palestinian Italian activist, Vittorio Arrigoni, last year, in an apparent attempt to secure the release of Saedni.
A number of Jihadist Salafi groups have surfaced in Gaza in recent years. Unlike Hamas, they endorse an ideology of global Jihad and some accuse Hamas of failing to implement Islamic laws in the coastal enclave.