The carrier will introduce “up to three” non-stop weekday services to Newcastle and Norwich, starting 1 September.
It will also offer non-stop Sunday services on both routes, which will serve the oil and gas industry.
Loganair says its new routes will target passengers “dissatisfied” by current Flybe franchise partner Eastern Airways services.
Citing CAA data, Loganair said a quarter of Eastern’s Aberdeen-Newcastle flights were cancelled last year while only 65.5% departed on time.
It is proposing early-morning northbound flights from Norwich to Aberdeen, with later returns, and has pledged to undercut Eastern’s return pricing.