The general manager of Broomhill informed clubs at a meeting on Monday night that he was resigning.
Fraser has been in the role for three-and-a-half years with a statement from the league noting during his time chair “he guided the league through some very difficult times including all the issues caused by the COVID pandemic”.
The Lowland League aims to appoint a new chair within the next week.
Graeme Mullin, vice-chair, said: “The work and effort that George has put in over the past few years is incredible.
“He has been an excellent chairperson of the league and is a well-respected figure within the game.
“George put in a huge amount of his own time into making the League stronger and better and he certainly succeeded in that regard.
“Everyone from the league wishes him well for the future.”