Hayya replaces Yahya al-Sinwar, who was killed in combat with Israeli forces in October 2024 as Hamas fought a full-scale two-year war with Israel in the Gaza Strip.
Hayya, the group's exiled Gaza Strip chief and top negotiator, has become an increasingly central figure in the leadership of Hamas since the deaths of Sinwar and Ismail Haniyeh, who was killed in Iran in July 2024.
He is seen as more hardline than Khaled Meshaal, the head of the group's office in exile and the other frontrunner for the leadership.
Hayya was among top Hamas officials targeted in 2025 in an Israeli attack in the Qatari capital Doha, where he is based, Israeli officials told Reuters.
Hayya was born in the Gaza Strip but in recent years has spent most of his time in Qatar.
Last year, the Israeli air force attempted to attack Hamas' top leadership in Doha, with Hayya reportedly one of the targets.
Four of his sons have been killed in Israeli attacks, including one in the attack in Doha.
The militant Islamist group faces some of the toughest challenges since it was founded in 1987, battered by two years of war ignited by its October 7, 2023, attack on Israel and facing international demands to disarm.
While fighting has abated in the Gaza Strip since the US-brokered ceasefire in October, Israel still holds more than 60 per cent of the coastal enclave, attacks continue, and conditions for the territory's two million people remain dire.
Israel says it targets Hamas and other Gazan militants who pose an imminent threat.
The office of Israeli Prime Minister Benjamin Netanyahu did not immediately comment on Hayya's selection.
On Monday, an Israeli strike killed at least three Palestinians driving in a vehicle in Khan Younis in the south of the Gaza Strip, medics said.
The Israeli military did not immediately comment.
The deaths add to a toll of more than 1150 Palestinians, mostly civilians, killed by Israeli attacks since the October ceasefire, according to Gazan health officials.
Four Israeli soldiers were killed by militants in the strip over the same period.
Hamas does not usually disclose its losses.
Since Sinwar was killed, Hamas has resorted to a five-member higher council that included Hayya and Meshaal in addition to three other officials.
The election of a Hamas chief is a lengthy process that began in January and was interrupted by the wars in Iran and Lebanon and continuing Israeli military operations in the Gaza Strip.
The selection is made by a 50-member council made up of Hamas members in the Gaza Strip, the occupied West Bank - including Israeli prisons - and those in exile.
Palestinian political analyst Reham Owda said Hayya's victory is a message that Hamas remains committed to armed struggle, rejects disarmament under any conditions and intends to rebuild its military strength while preserving its alliance with Iran and the so-called "Axis of Resistance."
"This indicates that negotiations related to disarmament are likely to face significant difficulties and obstacles," Owda told Reuters.
US President Donald Trump's ceasefire plan demands Hamas' disarmament and Israeli military withdrawals.
It foresees the Gaza Strip being run by a technocratic Palestinian administration overseen by Trump's Board of Peace.
But talks between Hamas, mediators, Egypt, Qatar, Turkey and Trump's Board of Peace envoys have so far failed to reach a broad agreement to end the conflict.
with DPA
