Loganair will cancel all flights running between the two airports from Friday, April 17 this year.
The decision has come after interest was "below expectations".
The airline also announced it will be launching a new route between Aberdeen and Haugesund in Norway.
Concerns have been raised before by people in the north-east of Scotland about the lack of connections between Aberdeen airport and London.
A petition demanding easyJet reinstate their Aberdeen to Gatwick flights has almost 5,000 signatures.
Rachel May, who launched the petition, said: "It is beyond ridiculous that we cannot connect to this major London Airport and makes no sense when every flight was packed so much so that often passengers were offered an incentive to take a different flight. We now have to find time consuming and expensive alternatives to get to Gatwick and quite honestly it is beyond a joke for a city the size of Aberdeen."
“We apologise to customers for the inconvenience caused and will work with them to put alternative travel plans in place, with the alternative of a full refund.
“Loganair remains committed to Aberdeen Airport, and will be pressing ahead with the launch of Aberdeen to Haugesund in Norway flights on 24 February.”
A spokesman for Aberdeen International Airport said: “We are disappointed at the news regarding Southend that the airline has stated is due low bookings.
“We are delighted Loganair remains committed to our airport with the new route launch of Aberdeen to Haugesund on February 24.
“Our passengers are still well connected to London via our Heathrow and Luton routes.”