In the final moments of the Siege of Fort Mifflin in November 1777, Colonel Samuel Smith (1752–1839) gives the orders to burn the remaining buildings before evacuating the fort. After the war is won, the Commandant's House is rebuilt in 1796. A Federal -era brick official residence with Georgian influence, this is to accommodate the commanding officer and his family. The most notable Commandant who lives here is Alexander Macomb (1782 – 1841), who serves here from 1802-1805.

In the two decades following the fort's decommissioning, it lay abandoned and open to trespassing explorers. It is October 26, 1980 when a group of Boy Scouts has a campout at the fort. Staying in the Commandant's House, they are cold and looking for warmth. Ignoring the signs that read "Do not use. Unsafe", they light a fire in the fireplace. The fire spreads through the historic building. The entire interior is destroyed, as well as the roof. In the early 2000's a major effort was made to restore the roof and cupola. It is once again open to the public, but on a limited capacity.