The flight will be operated using a Bombardier Canadair Regional Jet Series 200, which has a capacity of 50 passengers.
Commenting on the introduction of the flight, a South African Express statement said: "In line with the airline’s strategy to consolidate its domestic route network, focusing only on key markets, the airline will operate the Johannesburg – Port Elizabeth route every weekday, twice a day."
The regional airline currently flies to destinations such as Bloemfontein, East London and Walvis Bay from its bases at Cape Town, Johannesburg and Durban.
Its flights are incorporated in a strategic alliance with South African Airlink and South African Airways, although it remains operationally independent of South African Airways.
Last summer, the airline won the 2007 Annual Airline Reliability Performance Award at a prize ceremony in Canada hosted by Bombardier Aerospace.