Despite his request for an early retirement being accepted, pressure from his subordinates and President William Howard Taft led Barry to resign "for the good of the service".

[1][2] He studied at St. Francis Xavier College in New York City before entering the United States Naval Academy on July 21, 1865, through being an officer's son.

[3][4] Barry's stay at the naval academy was mediocre, being demerited for various incidents, including "very disorderly humming" and reading a newspaper during fencing lessons.

[2][3] Barry was aboard the USS Alaska during the blockade of Callao in 1880, witnessing the scuttling of Peruvian Navy ships Unión and Loa.

[2][5] He took part in the United States' first attack of the Spanish–American War on April 27, 1898, bombarding Spanish artillery batteries at the entrance of the harbor of Matanzas.

[1][8] Following the end of the war, Barry was assigned his first command role aboard the collier USS Marcellus, stationed in the New York Navy Yard.

[5][9] In the Philippine–American War, Barry's Vicksburg took part in an expedition to Palawan, led by Frederick Funston, in order to capture Filipino president Emilio Aguinaldo.

[26][27] There he participated in multiple inquiries, including the court-martial of Commander Charles C. Marsh, who accidentally led to the sinking of USS Yankee.

His notable actions included being bitten by an English Bull Terrier named "Bunk" who served as mascot of the USS Colorado and communicating with Glenn Curtiss regarding a possible naval aviation experiment.

[38] Initial speculation for the early timing was due to ill-health, but this was quickly dissipated the following day when the San Francisco Chronicle reported on Barry's officers discovering him a week before in a situation "of such a nature as to forbid explicit statement in print".

[39] Barry's suspected homosexuality was not explicitly reported in the newspapers, which instead referred to the matter as "concerning his moral character" and "the same vice which caused the downfall of Oscar Wilde".

[7][43] Poet T. S. Eliot referred to Barry in a letter to Ezra Pound on August 30, 1922: For below a voice did answer, sweet in its youthful tone, The sea-dog with difficulty descended, for he had a manly bone.

The Brooklyn Daily Eagle wrote a piece titled "Naval Academy Enrolls [Barry] as the Only Student Who Couldn't Read His Own Writing", and labelled his signature as the "weirdest in the Navy".