A law firm representing the teen filed the lawsuit on Monday and said their client is seeking $10 million from the city of Irving, Texas and $5 million from the Irving Independent School District.
Mohamed made national headlines when he took the clock to school in September and a teacher thought it was a bomb. He was arrested, but never charged.
The boy and his family have moved to Qatar, where a foundation is paying for his education.
Last month, he was invited to the White House where he and President Barack Obama spoke about outer space and the hope to get to Mars.
The Irving district attorney and city attorney have not commented about the lawsuit.