Henry Johnson enlisted in the United States Armed Forces on June 5, 1917 as a 5-foot-4-inch young man. This was almost two months after the American entry into World War I, joining the all-black New York National Guard 15th Infantry Regiment, which, when mustered into Federal service, was redesignated as the 369th Infantry Regiment, and was then based in Harlem. The 369th Infantry joined the 185th Infantry Brigade upon arrival in France, but was relegated to labor service duties instead of combat training. The 185th Infantry Brigade was in turn assigned on January 5, 1918, to the 93rd Infantry Division.

Although General John J. Pershing, Commander-in-Chief of the American Expeditionary Forces (AEF) on the Western Front, wished to keep the American forces autonomous, he "loaned" the 369th to the 161st Division of the French Army. Supposedly, the unreported and unofficial reason he was willing to detach the African-American regiments from U.S. command was that vocal white U.S. soldiers refused to fight alongside black troops.

The French Army needed more men and welcomed the reinforcements. The 369th Infantry regiment, later nicknamed the "Harlem Hellfighters", was among the first to arrive in France, and among the most highly decorated when it returned. The 369th was an all-black unit under the command of mostly white officers, including their commander, Colonel William Hayward. The idea of a black New York National Guard regiment had first been put forward by Charles W. Fillmore, a black New Yorker. Governor Charles Seymour Whitman, inspired by the brave showing of the black 10th Cavalry in Mexico, authorized the project. He appointed Colonel Hayward to carry out the task of organizing the unit, and Hayward gave Fillmore a commission as a captain in the 15th Infantry Regiment, New York National Guard. The 15th New York Infantry Regiment became the 369th United States Infantry Regiment prior to engaging in combat in France.

The French government awarded Johnson the Croix de guerre with a special citation and a golden palm. He was the first American soldier to receive the award.

In June 1996, Johnson was posthumously awarded the Purple Heart by President Bill Clinton. In February 2003, the Distinguished Service Cross, the Army's second highest award, was awarded to Johnson. John Howe, a Vietnam War veteran who had campaigned tirelessly for recognition for Johnson, and U.S. Army Major General Nathaniel James, President of the 369th Veterans' Association, were present at the ceremony in Albany. The award was received by Herman A. Johnson, one of the Tuskegee Airmen of WWII, on behalf of Henry Johnson, then believed to be his father; the mistake was not clarified until 2015, a decade after the younger Johnson's death, as part of the further research done leading up to the senior Johnson's Medal of Honor.

On May 14, 2015, the White House announced that Johnson would receive the Medal of Honor posthumously, presented by President Barack Obama. In the ceremony, held on 2 June 2015, Johnson's medal was received on his behalf by Command Sergeant Major Louis Wilson of the New York National Guard. Obama said, "The least we can do is to say, 'We know who you are. We know what you did for us. We are forever grateful.'"