Skinner had been at the helm at Christie Park since August 2018 after replacing Charlie Charlesworth.
The Black and Golds finished ninth in the 2018-19 season and were sitting 12th when last season’s campaign was declared over due to the coronavirus pandemic.
Huntly chairman Gordon Carter confirmed Skinner has decided to step down.
He said: “I can confirm tonight that Martin Skinner has today given notice of his resignation from his post as manager of Huntly Football Club.
“I respect his decision and therefore have accepted his resignation.
“On behalf of the club I would like to thank Martin for all his dedication and hard work since he took over the Manager’s role in August 2018.
“He leaves with the best wishes of everyone at the club.”