Lieutenant Commander John Allison is a native of Corpus Christi, Texas, and was also raised in Cherokee, North Carolina. In 1991, he graduated with honors from Flour Bluff High School in Corpus Christi, where he played football. He attended the University of Texas at Austin, earning a Bachelor of Science degree in Kinesiology with highest honors. He received his commission upon graduation through the Naval Reserve Officer Training Corps (NROTC) in December 1995.

John completed primary flight training at Naval Air Station (NAS) Corpus Christi, Texas, and transferred to NAS Kingsville, Texas, for intermediate and advanced jet training in the T-45 Goshawk. John earned his wings of gold in June 1998, and then reported to Strike Fighter Squadron 125 (VFA-125) at NAS Lemoore, California, for training in the F/A-18 Hornet. As a student assigned to VFA-125, he was awarded Fleet Replacement Pilot of the Year honors and several other awards for air combat, precision bombing, and carrier landing performance.

In February 2000, John reported to the VFA-192 "World Famous Golden Dragons" at Naval Air Facility (NAF) Atsugi, Japan, where he served as Naval Air Training and Operation Procedures Standardization (NATOPS) officer, aircraft division officer, air-to-air training officer, and head landing signals officer. While there, he earned 2002 VFA-192 Pilot of the Year honors, and deployed seven times aboard USS Kitty Hawk (CV 63), planning and participating in numerous international exercises with Japanese, South Korean, Thai, Singaporean and Australian Naval and Air Forces. John also deployed in support of Operation Enduring Freedom and flew combat missions supporting Operations Southern Watch and Iraqi Freedom.

In April 2003, John reported to the VFA-122 "Flying Eagles," based at NAS Lemoore, as an F/A-18 E/F Super Hornet instructor pilot. While at VFA-122, John served as the electronic briefing officer, assistant syllabus officer, plans officer, landing signals officer, and Tailhook Legacy demonstration pilot.