The Glasgow-based airline warned a loss was likely after the agreement between the two carriers ended last August, meaning Loganair could no longer fly under the Flybe banner.
The break-up with the largely domestic carrier left Loganair competing on six routes of its “largest routes”, including a number in the Highlands and Islands of Scotland.
"This year’s results bring to an end 17 consecutive years in profit for Loganair, and the fact that we forecast last year that we would be loss-making in 2017/18 makes it no less painful,” said Loganair chairman David Harrison.