The Israeli military and security forces received the coffin from the International Committee of the Red Cross inside the Gaza Strip, and it was to be sent to the Ministry of Health's National Centre for Forensic Medicine in Israel.
Israeli authorities said the family of the deceased would be notified first after a formal identification process.
The handover came after Hamas' military wing, known as the Qassam Brigades, said the remains were those of an "occupation prisoner", suggesting they belonged to an Israeli rather than one of the hostages of several other nationalities also taken in Gaza.
The handover of hostages' remains, called for under the ceasefire agreement, has been among the key sticking points — along with aid deliveries, the opening of border crossings into Gaza and hopes for reconstruction — in a process backed by much of the international community to help end two years of devastating war in Gaza.
This week, Hamas, in co-ordination with the International Committee of the Red Cross, has handed over to Israel the remains of nine hostages — along with a 10th body that Israel said wasn't that of a hostage.
The effort to find bodies followed a warning from US President Donald Trump that he would green-light Israel to resume the war if Hamas doesn't live up to its end of the deal and return all hostages' bodies, totalling 28.
In a statement on Friday, local time, Hamas said some hostages' remains were in tunnels or buildings that were later destroyed by Israel, and heavy machinery is required to dig through rubble to retrieve them.
It blamed Israel for the delay, saying it had not allowed any new bulldozers into the Gaza Strip.
On Friday, two bulldozers ploughed up pits in the earth as Hamas searched for hostages' remains in Hamad City, a complex of apartment towers in the city of Khan Younis.
Hamas urged mediators to increase the flow of aid into Gaza, expedite the opening of the Rafah border crossing with Egypt and start reconstruction.
It also called for work to "start immediately" on setting up a committee of Palestinian independents who will run the Gaza Strip and for Israeli troops to continue pulling back from agreed-upon areas.
The ceasefire plan introduced by Trump had called for all hostages — living and dead — to be handed over by a deadline that expired on Monday.
But under the deal, if that didn't happen, Hamas was to share information about deceased hostages and try to hand them over as soon as possible.
Israeli Prime Minister Benjamin Netanyahu has said Israel "will not compromise" and demanded that Hamas fulfill the requirements laid out in the ceasefire deal about the return of hostages' bodies.
At a news conference with his German counterpart in Ankara, Turkish Foreign Minister Hakan Fidan expressed concerns that Israel might use Hamas' "lack of equipment" to recover bodies as a pretext to resume hostilities.
Hamas released all 20 living Israeli hostages on Monday. In exchange, Israel freed around 2000 Palestinian prisoners and detainees.
In Israel, the Hostage and Missing Families Forum — which groups many families of hostages — said they will continue holding weekly rallies until all remains are returned.
Israel has also returned to Gaza the bodies of 90 Palestinians for burial. Israel is expected to turn over more bodies, though officials have not said how many are in its custody or how many will be returned.
