Mr Adams, who joined the company from Singapore-based Tiger Airways in 2013, said that for personal reasons it was the right time to go.
He will remain in the post until April. Loganair has started the process of finding his successor.
Chairman David Harrison said: "Stewart has been an extremely hardworking chief executive and he has provided strong leadership."
The Scottish airline flies under Flybe livery and operates 31 routes across the Highlands and Islands as well as other parts of the UK.
Loganair's chief executive Stewart Adams is stepping down.