Lieutenant Commander Charles Swift, 44, confirmed that he received word that he had been denied a promotion to navy commander "about two weeks after" the Supreme Court sided against the White House.
Under the military's "up or out" promotion system, Lieutenant Commander Swift will retire in March or April, closing out a 20-year career of military service.
A Pentagon appointee, Lieutenant Commander Swift embraced the alleged al-Qaeda's sympathiser's defence with a classic defence lawyer's zeal, casting his captive client as an innocent victim in the dungeon of King George, a startling analogy for the attorney whose commander-in-chief is President George W Bush.
He wore navy whites to his client's war crimes tribunal at Guantanamo, dress blues to challenge the administration on the steps of the Supreme Court and turned up last week at a symposium at Seton Hall Law School in more sobre, workaday khakis.
"It was a pleasure to serve," said the 44 year old, who added that he would defend Salim Hamdan all over again, even if he knew he would have to leave the navy earlier than he wanted.
"All I ever wanted was to make a difference - and in that sense I think my career and personal satisfaction has been beyond my dreams," he said.
Lieutenant Commander Swift, a University of Seattle Law School graduate, also said he will continue to defend Hamdan as a civilian.
The Seattle law firm of Perkins Coie, which provided pro bono legal work in Hamdan's habeas corpus petition, has agreed to support his defence of Hamdan in civilian life, he said.
Hamdan, 36, who has only a fourth-grade education, was captured along the border between Pakistan and Afghanistan while fleeing the US invasion of Afghanistan, launched in reprisal for the September 11, 2001 terrorist attacks.
He admits to working as Osama bin Laden's driver, and being paid US$200 (A$270) a month for the job on a Kandahar farm, but said he never joined al-Qaeda and never fought anyone.
Still at Guantanamo as an "enemy combatant", Hamdan halted his war crimes trial by challenging the format's constitutionality through civilian courts.
The justices ruled in June that President Bush had overstepped his constitutional authority by creating ad hoc military tribunals for prisoners at Guantanamo Bay, located in Cuba, sending the Pentagon back to the drawing board for the trials.
In the end, it developed a system very similar to those struck down, setting the stage for a likely new challenge this session.
Swift: “No brainer” for promotion
In the opinion of Washington DC lawyer Eugene Fidell, president of the National Institute of Military Justice, Lieutenant Commander Swift was "a no-brainer for promotion", given his devotion to the navy, the law and his client.
But, he said, Swift is part of a long line of navy defence lawyers "of tremendous distinction" who were not made full commander and "had their careers terminated prematurely".
Swift's supervisor, the Pentagon's chief defence counsel for Military Commissions, Colonel Dwight Sullivan, said it was “quite a coincidence” that the navy promotion board passed on promoting Swift “within two weeks of the Supreme Court opinion.”