The Prospect union said staff at AMSL - now part of Highlands and Islands Airports Limited (Hial) - had received "inferior terms".
The 48-hour strike will start from midday on 7 April.
Hial said its sites would be open as normal and the staff had been asked to consider a "realistic" pay claim.
The Scottish government-owned operator runs airports on the Western Isles, Orkney and Shetland, Argyll, Inverness and Dundee.
Hial said the union had sought a 30% pay claim, which the company described as "unreasonable".
Prospect has disputed the 30% figure and said its members were seeking 5% increase in pay and fairer overtime, weekend working and sick pay terms.
In a ballot, 87% of the union members voted in favour of a strike on a turnout of 85%.
Prospect national secretary Alan Denney said the date of the action avoided the busy Easter weekend.
He said: "The company and Scottish government should be in no doubt that members have had enough."
"Our dispute is with Hial and Scottish ministers, not passengers, so our representatives decided to avoid travel disruption over the Easter weekend."
In a statement, Hial said it had taken steps to improve pay, terms and conditions for AMSL staff.
It added: "We are prepared to discuss further improvements with Prospect.
"However, the union has refused Hial requests to enter into negotiations or consider a more reasonable pay claim."
Security staff working at Scotland's regional airports have voted in favour of taking industrial action over their terms and conditions, including pay.