The five weekly flights will launch on April 1 and will be flown under the Flybe brand as the airline is a franchise partner of Stobart.
The service will be operated on board a 72-seater ATR 72 and go daily on May 1 in the hope of cashing in on the summer season.
Cornwall airport Newquay managing director Al Titterington said: “It is great to see that further capacity will be added to the capital for 2019 thanks to Stobart Air’s decision to open direct flights to London Southend.
“During the first eight months of 2018 over 119,000 passengers have flown between CAN and Gatwick, a 12.8% increase over the same period of 2017.
"With the market between Cornwall and London continuing to go from strength-to-strength this new service comes at the perfect time.”
Stobart Air network development manager Ciaran Smith said: “The capital is currently underserved from the airport, so we are thrilled to launch this route, not only opening further options for people going directly to London, but also offering the people in the capital, plus Essex and throughout the East of England, better choice when travelling to Cornwall.”