He attended Dartmouth College, graduating Phi Beta Kappa with a Bachelor of Arts in 1977.
He earned a doctorate at the California Institute of Technology in 1981. After completing his postdoctoral work at the Massachusetts Institute of Technology, Hanlon joined the faculty of the University of Michigan in 1986. He moved from associate professor to full professor in 1990.
He was the Donald J. Lewis Professor of Mathematics.
He was the associate dean for planning and finance for the University of Michigan College of Literature, Science, and the Arts from 2001 to 2004 and the vice provost from 2004 to 2010. In 2010, he was appointed as the provost of the University of Michigan.
In June 2013 he became the 18th president of Dartmouth College. He serves on the editorial boards of the Journal of Algebraic Combinatorics and the Electronic Journal of Combinatorics.
While an undergraduate, he was a member of Alpha Delta, the fraternity that was a partial inspiration for the 1978 film Animal House.