Duffy served as chaplain for the 69th Infantry Regiment (known as the "Fighting 69th"), a unit of the New York Army National Guard largely drawn from the city's Irish-American population.

Duffy, who typically was involved in combat and accompanied litter bearers into the thick of battle to recover wounded soldiers, became the most highly decorated cleric in the history of the United States Army.

[4] Extremely popular with students, Duffy was part of a group of faculty members who introduced ground-breaking innovations into the seminary curriculum, putting the institution in the forefront of clerical education.

Already well known in theological circles, Duffy gained wider fame for his involvement as a military chaplain during World War I, when the 69th New York ("The Fighting 69th") was federalized again and redesignated the 165th U.S. Infantry Regiment.

Recognized by the regimental commander, Lieutenant Colonel William "Wild Bill" Donovan – who would go on to found the OSS in World War II – as a key element in the unit's morale, Duffy's role in the unit went beyond that of a normal cleric: the regiment was composed primarily of first- and second-generation Irish immigrants from New York City, many of whom wrote later about Duffy's leadership.

For tirelessly and unceasingly caring for the wounded and dying men in the village of Villers-sur-Fere, France, from July 28-31 1918, Chaplain Duffy was awarded the Distinguished Service Cross,[5] the citation for which reads: The President of the United States of America, authorized by Act of Congress, July 9, 1918, takes pleasure in presenting the Distinguished Service Cross to First Lieutenant (Chaplain) Francis Patrick Duffy, United States Army, for extraordinary heroism in action while serving as Chaplain with 165th Infantry Regiment, 42d Division, A.E.F., in the village of Villers-sur-Fere, France, from 28 to 31 July 1918.

Despite a constant and severe bombardment with shells and aerial bombs, he continued to circulate in and about two aid stations and the hospitals, creating an atmosphere of cheerfulness and confidence by his courageous and inspiring example.

[7] The citation for his Army DSM reads: The President of the United States of America, authorized by Act of Congress, July 9, 1918, takes pleasure in presenting the Army Distinguished Service Medal to Captain (Chaplain) Francis Patrick Duffy, United States Army, for exceptionally meritorious and distinguished services to the Government of the United States, in a duty of great responsibility during World War I. Chaplain Duffy performed with distinction his combined duties as Regimental and Division Chaplain, stimulating the work of all with whom he came in contact.

Whether in the front-line trenches or in an attack, he was with the troops, encouraging them to greater effort, an example of fearlessness and devotion to duty, helping to care for the sick and wounded, administering to the dying, and arranging for the burial of the dead.

New York, June 27 – The spirit of Father Francis Patrick Duffy, beloved chaplain of the 'Fighting Sixty-Ninth' of the wartime Rainbow Division, has rejoined the thousands of men who died on the battlefields of France where he served them.