Kilmer was born on December 6, 1886 in New Brunswick, New Jersey, the fourth and youngest child of Annie Ellen Kilburn (1849–1932) and Dr. Frederick Barnett Kilmer (1851–1934), a physician and analytical chemist employed by the Johnson and Johnson Company and inventor of the company's baby powder. Joyce was named Alfred Joyce Kilmer after Alfred R. Taylor, the curate; and the Rev. Dr. Elisha Brooks Joyce (1857–1926), the rector of Christ Church, the oldest Episcopal parish in New Brunswick, where the Kilmer family were parishioners. Rector Joyce, who served the parish from 1883 to 1916, baptised the young Kilmer. Kilmer's birthplace in New Brunswick, where the Kilmer family lived from 1886 to 1892, is still standing, and houses a small museum to Kilmer, as well as a few Middlesex County government offices.
Kilmer entered the Rutgers College Grammar School (now Rutgers Preparatory School) in 1895 at the age of 8. During his years at the Grammar School, he....
"...won the Lane prize in public speaking and was editor-in-chief of the Argo, the school paper. He loved the classics, although he had considerable difficulty with Greek. In his last year at Rutgers, he won the first Lane Classical Prize, a free scholarship for the academic course at Rutgers College, and one hundred dollars in money. Despite his difficulties with mathematics and Greek, he stood at the head of his class in preparatory school."
After graduating from the Rutgers College Grammar School in 1904, he continued his education at Rutgers College from 1904 to 1906. At Rutgers, Kilmer was associate editor of the Targum, the campus newspaper and a member of the Delta Upsilon fraternity. Unable to complete the rigorous mathematics requirement in the curriculum at Rutgers, facing a repeat of his sophomore year and under pressure from his mother, Kilmer transferred to Columbia College of Columbia University in New York City.
At Columbia, Kilmer was vice-president of the Philolexian Society, associate editor of Columbia Spectator, the campus newspaper, and was a member of the Debating Union. He completed his Bachelor of Arts (A.B.) degree and was graduated from Columbia on May 23, 1908. Shortly after graduation, on June 9, 1908, he married Aline Murray (1888–1941), a fellow poet to whom he had been engaged since his sophomore year at Rutgers. The Kilmers had five children: Kenton Sinclair Kilmer (1909–1995), Michael Barry Kilmer (1916–1927), Deborah ("Sister Michael") Clanton Kilmer (1914–1999) who was a Catholic nun at the Saint Benedict’s Monastery, Rose Kilburn Kilmer (1912–1917), and Christopher Kilmer (1917–1984).
Within a few days after the United States declared war on Germany and entered the first World War in April 1917, Kilmer enlisted in the Seventh Regiment of the New York National Guard. In August, Kilmer was initially assigned as a statistician with the U.S. 69th Infantry Regiment (better known as the "Fighting 69th" and later redesignated the 165th Infantry Regiment), of the 42nd "Rainbow" Division, and quickly rose to the rank of Sergeant. Though he was eligible for commission as an officer and often recommended for such posts during the course of the war, Kilmer refused stating that he would rather be a sergeant in the Fighting 69th than an officer in any other regiment.
In September, before Kilmer was deployed, the Kilmer family was met with both the contrary emotions of tragedy and rejoicing. The Kilmer's daughter Rose had died, and twelve days later, their son Christopher was born. Kilmer sailed to Europe with his regiment on October 31, 1917, arriving in France two weeks later. Before his departure, Kilmer had contracted with publishers to write a book about the war, deciding upon the title Here and There with the Fighting Sixty-Ninth. Kilmer wrote home, stating "I have not written anything in prose or verse since I got here - except statistics - but I've stored up a lot of memories to turn into copy when I get a chance." Unfortunately, Kilmer never was to write such a book. During his time in Europe, Kilmer did write prose sketches and poetry, most notably the poem "Rouge Bouquet", which was written after the First Battalion of the 42nd Division, which had been occupying the Rouge Bouquet forest northeast of the French village of Baccarat, which at the time was a quiet sector of the front—was struck by a heavy artillery bombardment on the afternoon of March 12, 1918 that buried 21 men of the unit, of which 14 remained entombed.
Kilmer sought more hazardous duty and was transferred to the Regimental Intelligence Section, in April 1918. He wrote to his wife, Aline that, "Now I'm doing work I love - and work you may be proud of. None of the drudgery of soldiering, but a double share of glory and thrills." According to Hillis:
"Kilmer's companions wrote: "He was worshipped by the men about him. I have heard them speak with awe of his coolness and his nerve in scouting patrols in No Man's Land.” This coolness and his habit of choosing, with typical enthusiasm, the most dangerous and difficult missions, led to his death."
During the Second Battle of Marne, there was heavy fighting throughout the last days of July 1918, and on July 30, 1918, Kilmer volunteered to accompany Major William "Wild Bill" Donovan when Donovan's First Battalion was sent to lead the day's attack.
During the course of the day, Kilmer led a scouting party to find the position of a German machine gun. When his comrades found him, some time later, they thought at first that he was peering over the edge of a little hill, where he had crawled for a better view. When he did not answer their call, they ran to him and found him dead. According to Father Duffy: “A bullet had pierced his brain. His body was carried in and buried by the side of Ames. God rest his dear and gallant soul.” Kilmer died, likely immediately, from a sniper's bullet to the head near Muercy Farm, beside the Oureq River near the village of Seringes, in France, on July 30, 1918 at the age of 31. For his valor, Kilmer was posthumously awarded the Croix de Guerre (Cross of War) by the French Republic.
Kilmer was buried in the Oise-Aisne American Cemetery and Memorial, near Fere-en-Tardenois, Aisne, Picardy, France. Although Kilmer is buried in France in an American military cemetery, a cenotaph is located on the Kilmer family plot in Elmwood Cemetery, in New Brunswick, New Jersey. A memorial service was held at St. Patrick's Cathedral in Manhattan.