The operator will initially use Fly Egypt for charter flights to Hurghada from Birmingham, Gatwick and Manchester from 14 October to mid-December.
Red Sea Holidays will then use European airline Enter Air for the Hurgada flight programme from mid-December to the end of April 2020.
Managing director Andrew Grant said: “We were aware of the problems Thomas Cook were facing, and plans were already progressing with alternative airlines to secure additional aircraft.
“Fly Egypt has the immediate capacity, operates a modern fleet of aircraft and allows us to quickly supplement the remaining operational flights out of the UK to Hurghada with three of our own.”