In the summer of 1777, British troops landed in Maryland. Those troops began marching toward Philadelphia, to seize the rebel capital. On September 11, 1777, the British troops, led by General William Howe, met up with, and defeated, George Washington´s Continental forces at the Battle of Brandywine. On September 26, the British had taken control of Philadelphia. The only hindrance to their crushing the Continental Army was a strained supply line.

To open up the supply line, the Delaware River, British forces laid seige to Fort Mifflin and Fort Mercer in early October, 1777. The seige which lasted until the middle of November, destroyed much of Fort Mifflin´s meager defenses. But the troops held their ground. By November 10, the British intensified their assault, launching an insessant barrage of cannonballs into the Fort. In the end, the troops could only hold out for so long, and they abandoned the Fort to the British on November 15 and 16, 1777. Because the troops held their ground for so long, though, the British had taken quarter in Philadelphia for the winter, while Washington could lead his troops to Valley Forge, a safe distance from British muskets.

Much of the restoration of Fort Mifflin began in 1795, under the presidency of John Adams. Many of the buildings standing today are holdovers from the post-1795 construction. During the Civil War, Fort Mifflin was used to house Confederate prisoners of war, and Union soldiers and civilians accused of breaking the law. The Fort served its country as late as the Korean War, in the 1950s. By 1962, Fort Mifflin was deeded back to the City of Philadelphia.