The first EgyptAir flight took off from Cairo to Doha on Monday following a reconciliation deal to heal more than of three years of a rift between Egypt and Qatar.
Egypt's official MENA news agency said that 38 passengers were aboard the Doha-bound plane.
Local media, citing EgyptAir sources, said the plane will return to Cairo at 04:50 local time (02:50 GMT), with 91 passengers aboard.
The sources said that four flights will be operated daily between Cairo and Doha.
On Jan. 12, Egypt reopened airspace to Qatari flights after Egypt, along with Saudi Arabia, the United Arab Emirates (UAE) and Bahrain, signed a reconciliation deal during the
Gulf Cooperation Council (GCC) summit on Jan. 5 to heal their dispute with Doha.
Flights between Saudi Arabia and Qatar have already resumed while the UAE and Bahrain also announced reopening their airspaces to Qatari flights.
During the Saudi-led blockade, Qatar was forced to direct most of its flights towards Iranian airspace in exchange for millions of dollars in transit fees.