At the breaking out of the Civil War he was in command of the Brooklyn Navy Yard.  He was overwhelmed with work for a time, and was glad when, early in the autumn of 1861, he was ordered to the West to help in the building of an inland navy on the Mississippi.

Captain Foote worked with the tremendous energy which he threw into every task, and succeeded in getting together seven boats, four of which were partly protected by armor.  At the beginning of February, 1862, he started from Cairo to ascend the Tennessee, his objective point being Fort Henry, though the Confederates were deceived into thinking it was Columbus, on the Mississippi.  He asked the Government for more men with which to man additional boats, but they were not furnished, and he went forward with such as he could get.

On the night preceding the attack on Fort Henry the little fleet anchored abreast of the army under General Grant, which was encamped on the bank.  The night was cold and tempestuous, but the morning dawned keen and clear, and no time was lost in preparing the flotilla for the attack on the fort.  He intimated to General Grant that he must not linger if he wished to cut off the retreat of the enemy.  Grant assured him he would be on time to put his army in motion.

Fort Henry stood on a bend in the river, which it commanded for a long distance up and down stream.  Foote placed his boats behind an island a mile below the fort, with a view of avoiding the long range rifles of the Confederates, which were liable to cripple the gunboats before they could get into close action.  The wooden vessels halted upon coming in view of the fort, and the ironclads, as they were called, moved slowly up stream abreast of one another, firing their bow guns in answer to the shots of the rebels.  The latter had had the time to practice to acquire the exact range, while the boats had yet to find it.  They fired slowly and with such accuracy that the infantry stationed outside of the works hastily fled, though the gunners bravely remained at their posts.

Foote opened fire when not quite a mile from the fort.  His instructions were to fire slowly and with care, the result of which was that guns were continually dismounted and the earth and sandbags sent flying in every direction.  It was while the attack was being pressed in this vigorous fashion that a shell pierced the boiler of the Essex, commanded by Lieutenant Porter, and caused so many deaths, as has been related in a preceding chapter.

This appalling accident was a serious loss to Captain Foote, for Porter was doing inestimable service when thus driven out of action, but the daring commander pressed forward in the face of the murderous fire, encouraged by the visible results of his shots, which were playing frightful havoc against the defences of the fort.  Tilghman, the Confederate commander, displayed great bravery, fighting until every one of his guns was dismounted.  Then, finding himself powerless to offer further resistance, he hauled down his flag.  Firing immediately ceased on the part of the Union flotilla, and Foote sent a boat ashore to take possession.