Johnston, who took over at NIFL in June 2013, will take the position as head of competitions and player status with the governing body in January.
"While the NIFL board and office bearers all wish Andrew well in his new role, it is disappointing for us to lose such a hard-working and dedicated managing director," the league said in a statement on Wednesday evening.
"Andrew will be with us until Friday 8 January and the NIFL board will meet in the coming weeks to collectively determine the next steps for the company."
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