The 10-year deal will see the airline operate in the Flybe colours from June.
Blue Islands will run six routes under the agreement: Southampton to Guernsey and Jersey; Guernsey to Jersey; Bristol to Jersey; London City to Jersey and a winter service from Jersey to Geneva.
More routes and aircraft could be added to the agreement if needed.
Flybe already operates franchises for Loganair and Stobart Air.
Saad Hammad, Flybe chief executive, said: “This third franchise agreement extends our ability to deliver unrivalled regional connectivity and time saving business travel for our customers and we look forward to welcoming everyone on board in June.
Rob Veron, Blue Islands managing director, said: “Guernsey and Jersey will enjoy increased exposure to potential new visitors thanks to Flybe’s huge marketing reach and wider distribution channels, bringing a boost to both visitor and business economies.
"What’s more, passengers will benefit from seamless connections with ‘through tickets’ from the Channel Islands for services to 30 UK and European airports in the Flybe network including Aberdeen, Dublin, Edinburgh, Belfast, and Amsterdam as well as summer destinations such as Faro and Malaga.
"Through tickets also mean significant APD savings when using connecting services."