Ahmed Mohamed was suspended after showing his clock to a teacher at his Irving, Texas, high school.
His case sparked an outcry on social media and attracted the attention of President Barack Obama and a number of tech companies like Google invited Ahmed to visit them.
Ahmed's family said in a statement today that it had pulled him and his two siblings out of the Irving school district "because of religious persecution," and had decided to home-school the kids.
They want justice and ensure that no family will ever have to experience what Ahmed went through, the statement said.
Two Dallas attorneys, Thomas Bowers and Reggie London, have been hired "to pursue Ahmed's legal rights and regain his science project from the Irving Police Department," it said.
No charges were filed against Ahmed, who on Tuesday visited Google's campus and this weekend will go to a United Nations summit. He also has been invited to the White House.