The carrier will begin flights from the Docklands airport on October 27 and expects to carry around 500,000 passengers a year.
From London City, Flybe will offer four daily services to Edinburgh and Dublin, three flights a day to Belfast and Exeter, and twice-daily services to Inverness.
This is the first time that Flybe has flown from London, with the new services augmenting its flights from other UK airports.
Flybe also intends to operate to European ski resorts and to French and northern Spanish destinations, with more details of these services expected soon.
Flybe chief executive Saad Hammad said: "Today's announcement is a significant landmark in the re-birth of Flybe. We are delighted to re-enter the London market at London's most convenient airport following a rigorous profitability analysis utilising our strict route assessment model.
"Dedicating five growth aircraft initially to these new routes is a major statement of intent and we look forward to building a successful and growing presence there over the coming years.
"Flybe is today already connecting over seven million passengers a year across the UK and Europe. With a major London connection, we reaffirm our place as the UK's largest regional airline."
London City Airport chief executive Declan Collier said: "We are poised for significant growth in the next 10 years - growth that will see us achieve 120,000 flight movements per annum, with an associated six million passengers by 2023.
"Today's announcement is an extremely important step on that journey."