Malthouse was appointed to the role in September, becoming the fourth Education Secretary in four months.
It is not yet clear if he resigned from the role or was asked to leave the Department for Education.
He wrote on Twitter: "As I leave the DfE, I do so with profound gratitude to officials, my private office team, and brilliant advisers, who all worked so hard. I hope my successor can harness their commitment to the most important mission in Whitehall: the future and welfare of our children."
He went on to thank "all the nursery workers, teachers, academics, staff, social workers and others, who help bring our young people through childhood and set them on a path to success. Our time together was short, but you will hear more from me in the months to come."
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