The 49-year-old Palestinian was greeted by members of his family and officials of the Islamist movement Hamas, including Parliament Speaker Aziz Duwaik.
Duwaik himself was only released in June after spending three years in Israeli prison, while Qafisha has spent a total of 10 years behind bars in several stints.
Hamas won 74 seats in the Palestinian parliament at the last election in 2005, when President Mahmoud Abbas' Fatah movement took only 45 places.
Israel arrested dozens of Hamas lawmakers across the West Bank after the Hamas members seized Israeli soldier Gilad Shalit in a cross-border raid in June 2006. Shalit remains in captivity to this day.
According to Hamas officials, 15 MPs are still held in Israeli prisons, including 12 from the Islamist movement.