The flight, which was operated the Egypt-based Aviary Aero and carried 184 passengers, arrived at the Hurghada airport amid tight security and preventive measures.
A number of Russian aviation companies have already obtained approval to land at the two Red Sea airports, sources at the Egyptian Holding Company for Airports and Air Navigation said.
Russia had resumed direct flights from the country to Hurghada and Sharm El-Sheikh in early August, shortly after President Vladimir Putin ordered the lifting of the six-year ban on direct flights to the Egyptian Red Sea resorts.
Moscow had suspended all flights to Egypt in October 2015 after a Russian plane crashed in Sinai, killing everyone on board.
Russia had resumed flights to Cairo in 2018, 30 months after the crash.
Since the crash, Egypt has upgraded its safety and security measures at all airports nationwide, and the country received several Russian security delegations to inspect safety measures at its airports.
Charter flights will help increase the flow of tourists from Russia to Egypt, the sources stressed.
Russian travellers are a major contributor to the country's tourism industry, a key source of hard currency.