VMU-3 is the third UAV unit in the Marine Corps established to provide reconnaissance and assist with deployments and training of ground units. A third of the UAV Operators from VMU-1 and VMU-2 were reassigned to VMU-3 to provide the foundation for the new squadron. In late September 2008, VMU-3 successfully flew the Shadow 200 UAV for the first time, and continues to fly missions in support of 3rd Marine Aircraft Wing, I Marine Expeditionary Force, and the Tactical Training Exercise Control Group (TTECG) on a regular basis.
VMU-3 was awarded the 2011 Commandant's Aviation Trophy for outstanding performance of a Marine aviation squadron.
VMU-3 completed its first overseas deployment to Iraq and the Helmand Province in Afghanistan in support of operations IRAQI FREEDOM/ENDURING FREEDOM in 2009-10. It was a part of the NATO ISAF Marine Corps forces in theater, and fell directly under Marine Aircraft Group 40, 2nd Marine Expeditionary Brigade. In 2011 VMU-3 completed its second OEF deployment.