BA CityFlyer operates scheduled and charter flights to the following destinations as of December 2020:
²¹

BA CityFlyer operates a number of weekend routes from regional airports as well as a program of charter flights on behalf of a number of tour operators:[7]
| Country | City | Airport | Notes | Refs |
|---|---|---|---|---|
| Salzburg | Salzburg Airport | Summer Seasonal | ||
| Chambery | Chambery Airport | Winter Seasonal | ||
| Toulouse | Toulouse–Blagnac Airport | Winter Seasonal | ||
| Venice | Venice Marco Polo Airport | Summer Seasonal | ||
| Verona | Verona Villafranca Airport | Summer Seasonal | ||
| Faro | Faro Airport | Summer Seasonal | ||
| Alicante | Alicante–Elche Miguel Hernández Airport | Summer Seasonal | ||
| Barcelona | Josep Tarradellas Barcelona–El Prat Airport | Summer Seasonal | ||
| Ibiza | Ibiza Airport | Summer Seasonal | ||
| Málaga | Málaga Airport | Summer Seasonal | ||
| Menorca | Menorca Airport | Summer Seasonal | ||
| Palma de Mallorca | Palma de Mallorca Airport | Summer Seasonal | ||
| Reus | Reus Airport | Summer Seasonal |
| Country | City | Airport | Notes |
|---|---|---|---|
| Copenhagen | Copenhagen Airport | ||
| Lyon | Lyon–Saint-Exupéry Airport | ||
| Paris | Orly Airport | ||
| Bremen | Bremen Airport | ||
| Hamburg | Hamburg Airport | ||
| Munich | Munich Airport | ||
| Gibraltar | Gibraltar Airport | ||
| Reykjavík | Keflavík International Airport | ||
| Milan | Linate Airport | ||
| Rome | Leonardo da Vinci–Fiumicino Airport | ||
| Venice | Venice Marco Polo Airport | ||
| Luxembourg | Luxembourg Findel Airport | ||
| Warsaw | Warsaw Chopin Airport | ||
| Granada | Federico García Lorca Granada Airport | ||
| Madrid | Adolfo Suárez Madrid–Barajas Airport | ||
| Birmingham | Birmingham Airport | ||
| Exeter | Exeter Airport | ||
| Isle of Man | Isle of Man Airport | ||
| Leeds/Bradford | Leeds Bradford Airport | ||
| Manchester | Manchester Airport | ||
| Newquay | Newquay Airport | ||