Mehta, who joined the think-tank after teaching at prestigious universities including Harvard and JNU, will join the Sonepat-based university in July.
"Yes, I have resigned from the Centre for Policy Research and will be joining Ashoka University," he said.
Mehta a well known scholar in the field of political science and education, has also taught at New York University School of Law.
He also served in several top-level government appointed bodies including the National Knowledge Commission and the National Security Advisory Board.
"Going forward, under the combined leadership of chancellor Rudrangshu Mukherjee and vice chancellor Pratap Bhanu Mehta, Ashoka University aspires to provide its students the highest quality liberal arts education and achieve its goal of becoming India's best university," the university said in a statement.