The Northern Irishman, who fills the vacuum left by the Belgian Tom Saintfiet, has extensive coaching experience in Africa.
He came out on top after 90 initial applications was eventually whittled down to three.
"The National Sports Council under the Ministry of Youth and Sports is delighted to announce the appointment of a Senior National Football Team Coach, in the person of Mr. Johnathan McKinstry," read a statement from the Gambian National Sports Council.
"In this regard, the general public is hereby informed that Johnathan McKinstry has been appointed on two years contract by the Ministry of Youth and Sports."
Gambia is the fourth African national side he will have taken charge of -- Sierra Leone the first in 2013, followed by Rwanda (2015-16) and Uganda (2019-2021).
His last coaching post was from 2022-2024 with Kenyan club side Gor Mahia.
Saintfiet announced in January he was stepping down after five-and-a-half years at the helm -- his contract ran till 2026 -- in which he guided the "Scorpions" to the quarter-finals of the 2022 Africa Cup of Nations in what was their maiden appearance.
