The 35-minute services from Kirkwall in Orkney in September and October will improve access for bird watchers.
The island is currently served only by air and ferry from Shetland.
Loganair operated the route from 1972 to 2006.
Loganair managing director Jonathan Hinkles said: “Our service through the autumn migratory season will cut hours from current journey times. It will be possible to leave Manchester or Edinburgh after breakfast and arrive in Fair Isle by lunchtime.”
Today's announcement was accompanied by the airline launching its own booking centre in Glasgow for travel from 1 September, when its franchise agreement with Flybe ends.
This has created ten new jobs, with credit card bookings no longer incurring extra fees.
Mr Hinkles said: “Launching our own reservations system today represents an important milestone in our progress to fly solo."