Khaled Meshaal described his first visit to Gaza as a “third birth”
He said his previous two “births” were the day he survived an assassination attempt by Israeli agents in Jordan in 1997, and his actual birth in 1956.
Mr Meshaal had not set foot in the Palestinian territories for decades.
His visit follows a ceasefire that ended days of violence between Israel and Hamas. The Islamist militant group has governed Gaza since 2007.
Mr Meshaal entered Gaza from Egypt at the Rafah border crossing, touching his head to the ground in celebration. Officials there said his wife had arrived late on Thursday.
In a statement to the media, he said: “I consider this moment my third birth, and I pray to God that my fourth birth will be the moment when all of Palestine is liberated.”
“Gaza is always in my heart,” he said.
Just after arriving in Gaza, Mr Meshaal inspected the charred remains of the car in which military commander Ahmed Jabari was killed in an Israeli strike last month.
He later visited Jabari’s home, and that of Hamas founder Sheikh Ahmed Yassin.
Jabari’s death marked the start of an eight-day Israeli offensive which Israel said was aimed at halting militant rocket attacks. Some 170 Palestinians and six Israelis were killed.
Hamas spokesman Sami Abu Zuhri said in a statement that Mr Meshaal’s visit was “a fruit of the victory of the resistance over the occupation”.
In the past, Egypt’s former president Hosni Mubarak never allowed him to use the Rafah border crossing to come here, and it was seen as too risky in terms of his personal security.
An Israeli official told the BBC that no guarantees for Mr Meshaal’s safety in Gaza had been requested and none had been given.
“Hamas is Hamas, it doesn’t matter who heads it,” said Foreign Ministry spokesman Yigal Palmor. “It’s position is known – violence as the only tool to promote its racist and extremist ideology.”
Israel, the US and the EU consider Hamas a terrorist organisation.
Leader in exile
Mr Meshaal also visited relatives of the Dalou family, 10 of whom were killed along with two neighbours in an Israeli air strike on Gaza City on 18 November.
Earlier, Human Rights Watch urged Israel to provide a full account of the incident, saying the man whom Israel said it had targeted, Mohammed Jamal al-Dalou, was a low-ranking police officer.
The Israeli military said the Dalou home had been a hideout for a senior “terror operative”, and that civilians were never a target.
For the centrepiece of his three-day tour, Mr Meshaal is scheduled to address a rally on Saturday in Gaza City, where a stage has been set up with a replica of a type of rocket Hamas has fired into Israel.
He is also expected to discuss reconciliation moves with the Fatah movement, which Hamas removed from Gaza by force in 2007 after winning elections there. Fatah now rules parts of the West Bank.
In 2011, Mr Meshaal and Palestinian Authority President Mahmoud Abbas – the Fatah leader – endorsed an Egyptian plan to reconcile the rival factions.
Although attempts to forge a Palestinian government of national unity have since stalled, Mr Meshaal told Reuters news agency ahead of his Gaza visit that “there is a new mood that allows us to achieve reconciliation”.
Barring a brief visit to the West Bank in 1975, Mr Meshaal had not visited the Palestinian territories since his family left in 1967.
He survived an Israeli assassination attempt in Jordan in 1997 only after the King Hussein demanded an antidote to poison used by Israeli agents.
Mr Meshaal became Hamas’s political leader in exile in 2004 when Sheikh Yassin was assassinated by Israel.
He ran operations from Damascus until February this year, when the unrest there prompted another move. He now bases himself in Qatar and Egypt.
Hamas was created in 1987 after the beginning of the first intifada – or Palestinian uprising – against Israel’s occupation of the West Bank and Gaza.
Under its charter, Hamas is committed to the destruction of Israel. But the group has also offered a 10-year truce in return for a complete Israeli withdrawal from territories it occupied in 1967.