In 1980, Duignan separated from active duty and joined the Air Force Reserve. When he was promoted to Brigadier General in 1998, he was the youngest General Officer in the U.S. Air Force Reserve. He currently holds the rank of Major General and is Commander, 4th Air Force, Air Force Reserve Command, March Air Reserve Base, California. He has thirteen wings, three groups and over 24,000 personnel assigned to his command. He is a command pilot with over 5,000 flying hours.

General Duignan is an Air Force Reserve Technician, a full-time federal civil service employee serving in a selected position within a military unit. He was appointed to the Senior Executive Service in 2002.

Significant assignments include:

• Deputy Commander for Operations, 459th Military Airlift Wing, Andrews AFB, Maryland
• Commander, 907th Airlift Group, Wright-Patterson AFB, Ohio
• Commander, 445th Airlift Wing, Wright-Patterson AFB, Ohio
• Deputy to the Chief of Air Force Reserve, Headquarters U.S. Air Force, Washington D.C.
• Director of Plans and Programs, Headquarters Air Force Reserve Command, Robins AFB, Georgia
• Commander, 4th Air Force, March ARB, California

Among the many awards and decorations he has received are:

• Distinguished Service Medal
• Legion of Merit with oak leaf cluster
• Meritorious Service Medal with two oak leaf clusters
• National Defense Service Medal with two bronze stars
• Southwest Asia Service Medal with bronze star
• Kuwait Liberation Medal (Kingdom of Saudi Arabia)
• Kuwait Liberation Medal (Government of Kuwait