EgyptAir is scheduled to operate four direct flights from Cairo to Tel Aviv every week from the beginning of October.
According to the Times of Israel, flights between the two cities are currently run by Air Sinai, in planes without the Egyptian flag.
The flights were to fulfil the terms of the peace deal, which was signed in 1979. However, despite the signing of the treaty, relations remained cool for decades meaning the flights were kept discreet.
Following President Abdel Fattah Al-Sisi's rise to power, relations between Cairo and Tel Aviv have warmed considerably and from October, the flights will be in fully marked aeroplanes.
Under Al-Sisi's presidency there has been significant security cooperation between the Egyptian and Israeli army in Sinai and last year Israel began transporting natural gas to Egypt under a $15 billion deal.
However, it has been hard for Egyptian authorities to convince the pro-Palestinian public that cooperation is a good idea.
Israel's Transport Minister Merav Michaeli has said that Sinai's Taba border, which also connects Egypt and Israel, will be allowing an unlimited number of people to pass through each day.
News of the flights comes after a meeting at the beginning of this week between Al-Sisi and the Israeli Prime Minister Naftali Bennett to discuss security and economic affairs and deepening relations.
It was the first official trip for a decade and the two met in the Red Sea resort of Sharm El-Sheikh.
The leaders discussed the situation in Gaza where Egypt helped broker a ceasefire after Israel's 11-day bombardment of the Strip.
Israel has maintained a crippling siege on the Gaza Strip since 2007 with the help of Egypt, which has kept the Rafah Crossing closed for long periods, even in the face of emergencies.