Howard was educated at Bowdoin College, but later attended West Point, graduating in 1854, ranked 4 out of 46 in his class. He was assigned in the ordnance as a 2nd lieutenant. After 2 years in the army, he returned to civilian life as a mathematics instructor at West Point.
At the outbreak of the Civil War, he was commissioned a Colonel in the 3rd Maine Infantry. He served at the 1st Bull Run and then joined Major Gen. George B. McClellan's Army of the Potomac for the Peninsula Campaign.
On June 1, 1862, while commanding a brigade at Fair Oaks, Howard was wounded twice in his right arm, which was subsequently amputated. He would be awarded the Medal of Honor in 1893 for his heroism at Fair Oaks. He recovered quickly enough to rejoin the army at Antietam, in which he rose to division command in the II Corps. He was promoted to major general in November 1862 and assumed command of the XI Corps the following April, replacing Major Gen. Franz Sigel. He also commanded the 2nd Division/II Corps at Fredericksburg.
At Chancellorsville, Howard suffered the first of 2 significant military setbacks. On May 2, 1863, his corps was on the right flank of the Union line, northwest of the crossroads of Chancellorsville. Gen. Robert E. Lee and Lieutenant Gen. Thomas J. "Stonewall" Jackson created an audacious plan in which Jackson's entire corps would march secretly around the Union flank and attack it. Howard was warned by Major Gen. Joseph Hooker, now commanding the Army of the Potomac, that his flank was "in the air", not anchored by a natural obstacle, such as a river, and that Confederate forces might be on the move in his direction. He failed to heed the warning and Jackson struck before dark, routing the XI Corps and causing a serious disruption to the Union plan.
At Gettysburg, the XI Corps, still chastened by its humiliation in May, arrived on the field in the afternoon of July 1, 1863. Poor positioning of the defensive line by one of Howard's subordinate division commanders, Brigadier Gen. Francis Barlow, was exploited by the Confederate Corps of Lieutenant Gen. Richard S. Ewell and once again the XI Corps was routed, forcing it to retreat through the streets of Gettysburg, leaving many prisoners behind. On Cemetery Hill, south of town, he quarreled with Brigadier Gen.Winfield S. Hancock about who was in command of the defense. Hancock had been sent by Major Gen. George G. Meade with written orders to take command, but Howard insisted that he was the ranking general present. Eventually, he relented. He started circulating the story that his corps' failure had actually been triggered by the collapse of Brigadier Gen. Abner Doubleday's I Corps to the west, but this excuse was never accepted at the time or by history—the reverse was actually true—and the reputation of the XI Corps was ruined. For the remainder of the battle, the corps remained on the defensive around Cemetery Hill, withstanding assaults by Major Gen. Jubal Early on July 2 and participating at the margin of the defense against Pickett's Charge on July 3.
Howard and his corps were transferred to the Western Theater to become part of the Army of the Cumberland in Tennessee. At Chattanooga, the corps joined the impulsive assault that captured Missionary Ridge and forced the retreat of Gen. Braxton Bragg. In July 1864, following the death of Major Gen.James B. McPherson, he became commander of the Army of the Tennessee, fought in the Atlanta Campaign, and led the right wing of Major Gen. William T. Sherman's famous "March to the Sea" Campaign, through Georgia and then the Carolinas Campaign.
After the Civil War, Howard served as Commissioner of the Freedmen's Bureau, and then went west to Oregon's Fort Vancouver, where he fought in the Indian Wars, particularly against the Nez Perce, with the resultant surrender of Chief Joseph. He became the Superintendent of West Point, commanded the Division of the East, and retired from the U. S. Army in 1894 with the rank of major general.
Howard is probably best remembered for founding Howard University. As Commissioner of the Freedmen's Bureau, he was known for promoting the welfare and education of slaves and freedmen. On November 20, 1866, ten members, including Howard, of various socially concerned groups of the time met in Washington, D.C., to discuss plans for a theological seminary to train African-American ministers. Interest was sufficient, however, in creating an educational institute for areas other than the ministry. The result was the Howard Normal Institute for the Education of Preachers and Teachers.
On January 8, 1867, the Board of Trustees voted to change the name of the institution to Howard University. He served as president from 1869 to 1874. He also founded Lincoln Memorial University in Harrogate, Tennessee, in 1895. He was considered a Christian soldier.