In September 2005, Pottinger joined the Marine Corps and served as a military intelligence officer. He was over-aged and out of shape when he joined. To meet the physical qualifications, he worked out with a Marine officer who was living in Beijing. He served three deployments: one (together with Mike Gallagher) in Iraq from April to November 2007, and two in Afghanistan from November 2008 to May 2009 and July 2009 to May 2010. On his second tour in Afghanistan, he met U.S. Army General Michael T. Flynn, with whom he co-wrote a report. The report, published in January 2010 through the Center for a New American Security, was titled "Fixing Intel: A Blueprint for Making Intelligence Relevant in Afghanistan". After he left active service, Pottinger worked in New York City, including for the hedge fund Davidson Kempner Capital Management.