The Guernsey-based airline, which previously had an agreement in place allowing it to use Flybe’s branding and website, says that it will formally announce the launch over the coming days.
The airline ran free-of-charge ‘goodwill’ flights for passengers stranded in both cities on Thursday and Friday.
In an update, a spokesman for the company, said: ‘Further announcements relating to commencement of a new Blue Islands scheduled service to Birmingham and Exeter from both Guernsey and Jersey will be announced over the coming days.
‘In the meantime, customers are assured of continued service to both of these destinations.’
It follows the announcement that Scottish airline Loganair was to take on Flybe’s seasonal Aberdeen and Inverness routes.
Flights to both cities will operate every Saturday with services to Aberdeen running from 9 May until 19 September and Inverness from 30 may until 19 September 2020.
However, no airlines have yet come forward to take on Flybe’s former route to Cardiff and ski-season service to Geneva.
As Blue Islands previously relied on the Flybe booking system, anyone wishing to book flights must now turn up to the Airport in person until their old booking platform has been reinstated.
A £50 one-way flat-fare structure has been implemented across their route network in the meantime.