Allen was born at Fort Belvoir, Virginia, on December 15, 1953; his father Joseph K. Allen, was a Navy veteran of World War II and the Korean war who retired as a lieutenant commander. He attended Flint Hill School in Oakton, Virginia. He graduated with military honors from the U.S. Naval Academy with the Class of 1976, receiving a Bachelor of Science degree in Operations Analysis. He is a 1998 Distinguished Graduate of the National War College. He holds a Master of Arts degree in National Security Studies from Georgetown University, a Master of Science degree in Strategic Intelligence from the National Defense Intelligence College, and a Master of Science degree in National Security Strategy from the National War College.
Following commissioning in 1976, Allen attended The Basic School and was assigned to 2nd Battalion, 8th Marines, where he served as a platoon and rifle company commander. His next tour took him to Marine Barracks, 8th and I, Washington, D.C. where he served at the Marine Corps Institute and as a ceremonial officer.
Allen then attended the Postgraduate Intelligence Program of the Defense Intelligence College, where he was the Distinguished Graduate. He subsequently served as the Marine Corps Fellow to the Center for Strategic and International Studies (CSIS). He was the first Marine Corps officer inducted as a Term Member of the Council on Foreign Relations.
Returning to the Fleet Marine Force in 1985, he commanded rifle and weapons companies and served as the operations officer of 3rd Battalion, 4th Marines. During this period he received the Leftwich Leadership Trophy. In 1988, Allen reported to the U.S. Naval Academy where he taught in the Political Science Department and also served as the Jump Officer and Jump Master of the Academy. In 1990 he received the William P. Clements Award as military instructor of the year.
Allen reported to The Basic School as the Director of the Infantry Officer Course from 1990 to 1992 and was subsequently selected by the Commandant of the Marine Corps Fellows Program, which provides "assignment to either a prominent national foreign policy/public policy research institution or to a national security studies program at a selected university". Allen has served as a special assistant on the staffs of the 30th Commandant of the Marine Corps and the Commanding General, Marine Corps Combat Development Command. In 1994, he served as the Division G-3 Operations Officer for the 2nd Marine Division and subsequently assumed command of 2nd Battalion, 4th Marines; re-designated as 2nd Battalion, 6th Marines. This unit served with JTF-160 in Operation SEA SIGNAL during Caribbean contingency operations in 1994, and as part of the Landing Force of the 6th Fleet in Operation JOINT ENDEAVOR during Balkans contingency operations in 1995–1996.
Following battalion command, Allen reported as the Senior Aide-de-camp to the 31st Commandant of the Marine Corps, Charles C. Krulak, ultimately serving as his military secretary.
He commanded The Basic School from 1999 to 2001, when he was selected in April 2001 to return to the Naval Academy as the Deputy Commandant. Allen became the 79th Commandant of Midshipmen in January 2002, the first Marine Corps officer to serve in this position at the Naval Academy. In January 2003 Allen was nominated for appointment to the rank of brigadier general.
Allen's first tour as a General Officer was as the Principal Director, Asian and Pacific Affairs in the Office of the U.S. Secretary of Defense, a position he occupied for nearly three years. From 2006–2008, Allen served as Deputy Commanding General, II Marine Expeditionary Force and Commanding General, 2nd Marine Expeditionary Brigade, deploying to Iraq for Operation Iraqi Freedom 06-08, serving as the Deputy Commanding General of Multi-National Forces West and II MEF (Forward) in the Al Anbar Province, Iraq. In January 2007 Allen was nominated for appointment to the grade of major general.
In June 2008, Secretary of Defense Robert Gates announced Allen's nomination for promotion to the rank of lieutenant general. He served as the deputy commander of the U.S. Central Command from July 15, 2008, until July 18, 2011, at MacDill Air Force Base. On June 30, 2010, Allen temporarily commanded Central Command after General David Petraeus left to assume command of the International Security Assistance Force in Afghanistan. He served as acting commander until General James Mattis took command on August 11. Allen was promoted to general by Chairman of the Joint Chiefs of Staff, Admiral Mike Mullen prior to his assumption of command of ISAF, and U.S. Forces Afghanistan (USFOR-A) on July 18, 2011.
Foreign awards include the Mongolian Meritorious Service Medal, First Class; the Polish Army Medal in Gold; and the Taiwan Order of Cloud and Banner with Special Cravat.
On March 6, 2012, he received the Polish Afghanistan Star Medal from Polish President, Bronisław Komorowski.
On April 20, 2012, he received another Polish award, the Commander's Cross of the Order of Merit of the Republic of Poland.
In November 2012, he came under investigation for possible "inappropriate-communication" concerning his correspondences with Jill Kelley, the Honorary Ambassador to U.S. Central Command Coalition Forces. In response to the investigation, Secretary Panetta suspended his confirmation hearing for commander of EUCOM and requested the U.S. Congress to speed the confirmation of General Joseph F. Dunford, Jr. to command of forces in Afghanistan. On January 22, 2013, General Allen was cleared in a misconduct inquiry.
On February 10, 2013, Allen relinquished command of the International Security Assistance Force and U.S. Forces Afghanistan (USFOR-A) to General Dunford.
On February 19, 2013, U.S. President Obama accepted Allen's request to retire from the military as his wife fell seriously ill.
On April 29, 2013, Allen's official retirement ceremony was held at the United States Naval Academy. After leaving the military in 2013, Allen continued to work as an advisor to Secretary of State John Kerry and former Defense Secretary Chuck Hagel.
On September 11, 2014, the Obama Administration announced that Gen. Allen would coordinate international efforts against the Islamic State in Iraq and Syria. Allen would be named as the Special Presidential Envoy for the Global Coalition against ISIL. With the Obama administration investing 500 million U.S. dollars in the program, Gen. Allen constructed 'Platoon 30', which attempted to conscript and train fighters. However, the Platoon failed to reach its goal of conscripting 5,400 fighters, only managing to conscript a few hundreds, of whom 75 deserted to join Jabhat Al-Nusra in the Platoon's second mission.
On October 23, 2015, the White House announced his departure from the post, to be was succeeded by Brett McGurk of the State Department.
After government service, Allen joined the Brookings Institution as senior fellow and co-director of the Center for 21st Century Security and Intelligence.
Allen is a member of the Homeland Security Advisory Council.
Allen was a featured speaker at the 2016 Democratic National Convention in Philadelphia on July 27, 2016, on the topic of national security. He criticized Republican nominee Donald Trump and endorsed Hillary Clinton for President. Trump fired back, "He [Allen]’s a failed general."
Allen's personal decorations include the following: