The new route will launch on June 25 and initially operate twice weekly over the summer period on Mondays and Fridays.
The airline said it would offer an important link for business travellers, holiday makers and those visiting friends and relatives as Covid regulations ease, as well as for cargo.
In a statement, the airline said it will also launch a twice-weekly service to Jersey from London City Airport.
Tom Stoddart, Managing Director of BA CityFlyer, which will operate the new services, said: “It’s great to be able to launch these two new services to Gibraltar and Jersey – it’s something customers have been asking us to do for quite a while.”
“Whether it’s for a holiday or visiting friends or relatives who live either end of route when the time is right, customers will benefit from direct flights to and from the extremely conveniently located London City Airport.”