Filkins has received two George Polk Awards, given annually by Long Island University to honor contributions to journalistic integrity and investigative reporting. He was cited for his reports from the assault on Fallujah, Iraq, in November 2004, when the Marine company he travelled with lost a quarter of its men in eight days. In 2011, Filkins and "The New York Times" colleague Mark Mazzetti won for their reporting on Afghanistan and Pakistan.