Baker was born in Davenport, Iowa, and attended Moline High School from 1963 to 1966. At 5' 1", he was a gymnast before joining the army. He became a "tunnel rat" in Vietnam, a soldier who entered Viet Cong tunnels searching out the enemy and destroying their caches of war material. Baker made the military his career, retiring in 1989. He then began working as a computer analyst at a Veterans Hospital in South Carolina. In addition to serving as the Vice-President of the Congressional Medal of Honor Society, he served as a member on the Nation's Monuments and Cemeteries Committee.

Baker entered the U.S. Army in Moline, Illinois, serving as a private in A Company, 2nd Battalion of the 27th Infantry Regiment, 25th Division. In Vietnam, he took part in Operation Attleboro which began in September 1966. On November 5, 1966, Baker and his unit were called to assist another squad who were taking enemy fire. En route, A Company began to take fire and lost their lead soldier. Together with two other soldiers, Baker took over the head of the column and assisted in destroying two enemy positions. They were moving to take two others when a hand grenade knocked Baker off his feet.

With the two other soldiers wounded, Baker "single handedly" destroyed another bunker before recovering his comrades. Despite taking further fire from enemy bunkers and snipers, he continually fell back to replenish ammunition and take back several wounded. For these actions, he was awarded the Medal of Honor along with Captain Robert F. Foley, who also received the Medal of Honor for his actions in the battle. When awarding the medal, President Lyndon B Johnson stated:

The battlefield is the scarred and the lonely landscape of man's greatest failure. But is a place where heroes walk. Today we come here to the East Room of the White House to honor two soldiers, two soldiers who—in the same battle and at the same time—met the surpassing tests of their lives with acts of courage far beyond the call of duty. Captain Foley and Sergeant Baker fought in the same company. Now, together, they join the noblest company of them all. They fought because their Nation believed that only by honoring its commitments, and only by denying aggression its conquest, could the conditions of peace be created in Southeast Asia and the world.^[4]

 

In 2008, the I-280 Bridge, connecting Davenport, Iowa with Rock Island, Illinois, was renamed the Sergeant John F. Baker Jr. Bridge in his honor.^[1]

In 2018, the Rock Island Arsenal in Rock Island, Illinois put his name on a street in its new Eagle Point Housing Area. ^[2]

Baker suffered from heart problems in the last years of his life and began using oxygen in 2010. He died aged 66