The renowned art school was extensively damaged last June while it was undergoing a £35 million restoration following a previous fire in May 2014.
Ms Gray, whose husband has cancer, said on Friday that she is stepping down from her role "for personal family reasons".
Professor Nora Kearney, currently vice-chairwoman, will take over as interim chairwoman.
Ms Gray said: "I have advised the board of governors of the Glasgow School of Art that I will be taking a temporary period of absence both as chair of the board and as a lay governor for personal family reasons.
"Given the challenges the school has faced over the past 12 months this was an incredibly difficult decision to take.
"The Glasgow School of Art is an amazing institution, full of remarkable, committed and creative people who continually give above and beyond, and I look forward to working with everyone again during the next academic year.
"Professor Nora Kearney, currently vice-chair, will take over as interim chair in my absence."
Ms Gray gave evidence to Holyrood's Culture Committee last November when she said the art school plans to rebuild the Mackintosh building exactly as it was designed 100 years ago.
In its report published in March, the committee said there should be wider consultation on this, with the cost of the project estimated at around £100 million.