In November 1951, during the Korean conflict, A. Jay Cristol joined the US Navy as an aviation cadet, earning his Navy Wings of Gold in April 1953. He deployed with VS-37, a Navy anti-submarine squadron aboard the aircraft carrier Princeton (CV-37) to the Western Pacific and the Sea of Japan. He was also part of TG70.4 during February 1955, in support of evacuating Nationalist Chinese from the Tachen Islands near the Communist China mainland in the South China Sea. He flew day and night missions as both a hunter pilot flying the Grumann AF-2W and a killer pilot flying the Grumann AF-2S. He was subsequently attached to the Fleet All Weather Training Unit, Pacific at San Diego, California as an instrument flight instructor and taught maneuvers for the delivery of nuclear weapons. Upon returning to civilian life, Cristol joined the Naval Air Reserve where he qualified as a four-engine Navy transport plane commander. In the 1960s, he flew operational flights during the Cuban Missile Crises and volunteer airlift missions to Vietnam.

After 18 years as a Naval aviator, Cristol joined the Judge Advocate General's Corps. He graduated with distinction from Naval Justice School. He served as a lawyer for another twenty years. His duties included teaching law of war and serving as the administrative officer for the summer Naval Reserve law courses. In 1983, he was made an honorary professor by the Naval Justice School. He has performed special active duty in the office of the Secretary of the Navy and the Chief of Naval Operations. In the 1980s, the Department of Defense sent him to the International Institute of Humanitarian Law at San Remo, Italy to lecture on Law of Naval warfare to senior foreign military officers. Captain Cristol retired in 1988. He wears more than a dozen military decorations including the Meritorious Service Medal, the Navy Commendation Medal, and the Navy Achievement Medal.

In civilian life, Cristol became a lawyer and practiced civil law. He served as Special Assistant Attorney General of Florida during the 1959, 1961, 1963, and 1965 sessions of the Florida Legislature. In 1985, after 25 years of law practice, he left his position as senior partner in a firm he founded to accept an appointment to the federal bench. He continues to serve as Chief Judge Emeritus in the Southern District of Florida. He is also an adjunct professor, teaching at the University of Miami School of Law.

An interest in international terrorism led him to enroll in the Graduate School of International Studies of the University of Miami where he researched and wrote on terrorism. Because of his background as a navy pilot, a navy lawyer (JAG), a lecturer in law of naval warfare, a civil lawyer, and a federal judge, members of the faculty encouraged him to research and write about the Liberty incident. He spent ten years researching the subject and was awarded a Ph.D. by the University of Miami Graduate School of International Studies. His collection of research material on this subject is considered to be the largest and most complete of any collection on the subject in the entire world. After completing his dissertation, he obtained declassification of additional heretofore secret documents through many Freedom of Information Act requests and appeals and then by suing the National Security Agency under the Freedom of Information Act. He prevailed, resulting in the release of audio tapes and documents of substantial importance to his research on July 2, 2003. This release made international news including an Associated Press story and two CNN appearances by Cristol (including 15 minutes live with Wolf Blitzer). His book, The Liberty Incident, was written to update and complete the historical record. He was invited by the United States Department of State to an international conference on the 1967 war. He appeared on a panel about the Liberty incident together with the Historian for the State Department, the Historian for the Central Intelligence Agency (CIA), and the Historian for the National Security Agency (NSA). The event was broadcast live by C-SPAN, and BBC World News broadcast a live interview of Cristol. The Department of State released Volume XIX of Foreign Relations of the United States which includes substantial additional declassified documentation, all of which support Cristol's conclusions. He has written numerous articles on law, aviation, history, and other subjects.

Judge Cristol remains an avid aviator. He made his first flight in a Piper J-3 Cub on Biscayne Bay in 1945. He has personally piloted a Ford Tri-Motor, the Goodyear Blimp, a Soviet MiG-15, a Czech L-39, a Chinese CJ-6, a French Fouga Magister, and many other unique, antique, or historic aircraft. In 1998, he became one of the few persons to have an airplane named after him when Pan Am named one of their 727 aircraft the Clipper A. Jay Cristol. After presiding over the reorganization of Arrow Air, he was further honored by having an Arrow Air DC-8-62 named the "Judge A. Jay Cristol." He is a founding member of the National Museum of Naval Aviation at the Naval Air Station in Pensacola, Florida and a founding member of the Wings Over Miami Military and Classic Aircraft Museum in Miami, Florida. Cristol is an Angel Flight volunteer pilot and enjoys flying people in need of transportation to and from regional medical centers for treatment. In 2003, the Greater Miami Aviation Association honored Judge Cristol with their Glenn Curtiss Award for having a profound effect on the aviation industry and for his contributions to improve the South Florida community. On February 1, 2007, St. Thomas University School of Law honored Judge Cristol with its Outstanding Jurist Award. The Miami Herald featured Judge Cristol on November 13, 2006, in an article describing him as "a renaissance man". The 2007 May/June issue of Airliners magazine published a story about Judge Cristol; and, Dow Jones featured Judge Cristol on January 2, 2008 in a three page article.