A native of Philadelphia, Rubin earned a Ph.D. in history from Yale University in 1999. His dissertation, The Making of Modern Iran, 1858–1909: Communications, Telegraph and Society won Yale's John Addison Porter Prize.

Rubin has lectured in history at Yale University, Hebrew University, Johns Hopkins University, and worked as visiting lecturer at Universities of Sulaymaniyah, Salahuddin, and Duhok, in the Kurdistan Region of Iraq. Between 2002 and 2004, Rubin worked as a country Director for Iran and Iraq in the Office of the Secretary of Defense, from which he was seconded to the Coalition Provisional Authority in Iraq. Rubin currently teaches senior U.S. Army, U.S. Marine, and U.S. Navy leadership prior to their deployment to Iraq, the Persian Gulf, and Afghanistan.

Between 2004 and 2009, he was Editor of the Middle East Quarterly. He has received fellowships from the Council on Foreign Relations, and the Carnegie Council for Ethics in International Affairs.

In December 2017, Turkish national offered a reward of 3-million Turkish lira (almost $800,000) for help in delivering Rubin to Turkey to answer Turkish terrorism allegations in connection with the 2016 Turkish coup d'état attempt.