Direct proof of use
The GBU-31 JDAM was used by U.S. air forces in Afghanistan during Operation Enduring Freedom. A Mountain Home Air Force Base history states that the 34th Bomb Squadron opened the war on October 7, 2001 with B-1B Lancers loaded with GBU-31 Joint Direct Attack Munitions, and says the squadron released more than 6.9 million pounds of munitions against Taliban and al-Qaeda targets during its first three months in theater.
Later U.S. Air Force airpower summaries document individual Afghanistan strikes with GBU-31s. On November 28, 2007, an F-15E dropped a GBU-31 in Bari Kowt, a B-1B used a GBU-31 and GBU-38s against firing positions in Garmsir, and an F-15E used a GBU-31 and GBU-38s in Kandahar.
Sources: Mountain Home OEF Start, Nov. 28 Airpower Summary
Narrative
In the Afghanistan theater, the GBU-31 appears in official sources as an air-delivered precision munition used from bomber and strike-fighter platforms. Opening-war accounts connect B-1B Lancers carrying GBU-31s to attacks on Taliban and al-Qaeda targets, while later airpower summaries show the weapon employed in close air support for International Security Assistance Force, Afghan security forces, and coalition troops.
The documented target sets in these summaries include cave entrances, enemy defensive positions, firing positions, rocket positions, enemy personnel, and fighting positions. The public daily summaries normally identify the munition as GBU-31 or guided bomb unit-31, but they do not specify whether each strike used the Mk 84 general-purpose or BLU-109 penetrator body.
Sources: Mountain Home OEF Start, Oct. 4 Airpower Summary, Oct. 8 Airpower Summary, Nov. 28 Airpower Summary, June 22 Airpower Summary