Suvidha supermarkets in southern Palestine opened on Monday after the government agreed to a cease-fence deal with Hamas.
In the northern coastal enclave, a cease fire between Hamas and Israel has been in place since July.
The new stores will offer fresh produce, fresh meat and vegetables.
Israel has also set up a new food distribution centre in the coastal enclave to provide fresh produce to households in Gaza.
Israel imposed a two-week closure on Gaza in January after it refused to allow the entry of food products into the enclave.
The Israeli government says it has launched an operation in the Gaza Strip to destroy tunnels used by Hamas militants.
The international community condemned the Israeli operation in Gaza on Monday, saying the blockade on the coastal strip was unlawful.
The Palestinian territory has been gripped by violence since 2007, when Hamas fighters and other militant groups took over the territory, with Israel declaring a three-day state of emergency and launching a series of air raids on Hamas positions in the enclave to stop it firing rockets.
In November, Israel struck a rocket launch site in the northern Gaza Strip, killing three civilians.
The Gaza Strip has been divided into two main regions, called Rafah and Gaza City, since the outbreak of hostilities in July 2007.
Israel says it does not recognise the Palestinian territories, and Hamas and other Islamist groups have said they will not recognise it either.
The agreement signed on Monday also includes an agreement on Palestinian refugees, including those who fled their homes during the conflict.
The government has agreed to pay $300m to help the Palestinian refugee population of Gaza rebuild, according to the agreement signed by Prime Minister Benjamin Netanyahu and Palestinian President Mahmoud Abbas.
Palestinian officials have said the deal will provide $100m in aid to the Palestinian Authority (PA), while the government is also pledging $1bn in assistance for reconstruction efforts.
Israel is also expected to release 2,000 prisoners, who are being held on the Israeli side of the Gaza border, and lift a temporary moratorium on all Israeli-Palestinian negotiations.
Hamas, the Islamic militant group that controls Gaza, has been fighting for an independent Palestinian state since 2007.
It is believed to have around 200,000 fighters in Gaza, including some 10,000 in the West Bank.
Israel launched its military offensive on July 8 in response to rocket fire from Gaza.
Israel’s operation killed at least 80 people, most of them Palestinians.
In December, Israel announced the death toll had risen to more than 1,000 after a series tolled and damaged dozens of homes.
Israel has been criticised for the violence, with the UN estimating that at least 1,400 Palestinians have been killed since the fighting began in July.