He will be succeeded immediately by vice-president Jim Ballantyne.
The former Partick Thistle director has been embroiled in controversy since it was revealed he was a director of Stenhousemuir while his family held shares in Thistle.
League rules do not allow anyone to have an interest in more than one club.
And, though McMaster transferred his Thistle shares to his children after he joined the Stenhousemuir board last year, an investigation was launched to determine if he had contravened any rules.
McMaster made no mention of the shares when he announced his resignation after two-and-half years as president.
In a statement issued through the SPL, he said: “I am sorry to be standing down at this time, but I have always been someone who fully commits to anything I am involved in, and my personal circumstances make it impossible for me to do so at the Scottish Football League at present.”
Chief executive David Longmuir said: “Brown has carried the office of President of the Scottish Football League with distinction and skill.
“I believe the organisation is now stronger, more together, and more attractive to sponsors than before, and I attribute much of that progress to Brown.”
Airdrie United chairman Ballantyne is now ready to carry on the difficult work and said: “Brown stood up to the plate at a time of great anxiety in Scottish football when change was needed and it is extremely relevant to compare the state of the SFL now and the SFL then.
“The amount of man-hours he has devoted to the SFL in his term of office is staggering despite most of it going unnoticed.
“He will leave the SFL in great shape in difficult economic times and I will do my utmost to carry on his good work.”
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