Flybe will operate a four-times-daily service to and from Edinburgh and Dublin, a three-times-daily service to and from Belfast and Exeter and a twice-daily service to and from Inverness.
The airline is targeting business travellers as part of its London expansion plans. Saad Hammad, CEO of Flybe, said: "Our new London City routes provide direct links for customers in the regions to the heart of London's financial district."
Flybe will hold a launch event today at London City Airport, under the "Spirit of the Regions" theme.
Flybe is expecting to fly more than half a million passengers annually on its routes to and from London City Airport after it launched a new Amsterdam service earlier this year.