“Salah Al-Aruri was elected deputy to (Hamas leader) Ismail Haniya,” an official in the movement said, after a vote of its 18-member political bureau.
Al-Aruri, who lives in exile after having spent almost two decades in Israeli jails, is alleged to have masterminded a series of attacks against Israelis in the occupied West Bank.
In 2015, the US Treasury issued sanctions against Al-Aruri, along with other officials of Hamas, which is currently in negotiations with the internationally recognized Palestinian Authority about reconciliation.
Al-Aruri was based in Syria for a number of years but is now resident in Lebanon, according to senior Hamas sources.
There was no immediate reaction from Israel, which had previously accused Turkey of sheltering Al-Aruri, to his appointment.
Al-Aruri’s appointment follows the election in February of another military leader, Yahya Sinwar, as Hamas’s Gaza chief.
Analysts say Sinwar is technically third in command following Al-Aruri’s appointment but has strong support in the military wing.
Al-Aruri joined Hamas in 1987 and helped establish a military wing for the movement in the West Bank, according to Hamas media.
He was jailed by Israel for 15 years after being convicted of forming military cells in the territory.
Three months after his release in 2007, he was again jailed for a further three years, before being released and deported from the Palestinian territories.
Al-Aruri’s appointment came as Palestinian Prime Minister Rami Hamdallah left the Gaza Strip on Thursday after a four-day visit aimed at reconciliation with Hamas.
Hamas agreed to hand over power to a unity government last month and Hamdallah’s visit, the first since 2015, saw his ministers take control of ministries in Gaza.
The move is part of wider attempts to end a split between the internationally recognized Palestinian Authority, which is based in the occupied West Bank, and Hamas, which runs Gaza.
The two sides are set to meet for further talks in the Egyptian capital Cairo on Tuesday.
Before leaving on Thursday morning, Hamdallah and a number of his ministers visited the largest hospital in the Gaza Strip, as well as a desalination plant.
He then left with his ministers through the Erez crossing in northern Gaza, which is controlled by Israel, an AFP videographer said.
Hamas, in a statement, said: “The Gaza Strip and its ministries are under the administration of the national reconciliation government. Hamas will work to support and strengthen its role.”
Mohammed Dahlan, who played a key backroom role in a major new effort for Palestinian unity, told Reuters that a two-state peace agreement with Israel was impossible and healing wounds from a civil war that split Palestine was now a priority.
Dahlan, a member of the Fatah party, spoke to Reuters after the unity Cabinet held its first meeting in the enclave in three years.
“The internal Palestinian situation is more sacred, is more important and is more useful now than the so-called negotiation,” the veteran politician said of talks with Israel that collapsed in 2014 over issues such as Israeli settlement-building in occupied territory and Fatah-Hamas reconciliation.
Dahlan, 56, said: “There is a complete Judaization of the West Bank, not only of Jerusalem. It has become impossible for the two-state solution to be implemented. Therefore, there is no political horizon.”