On November 14, 2003 the Clifton Inn suffered a fire that killed two law firm recruiters staying at the hotel and injuring two other guests. The fire caused an estimated $250,000 in structural damage to the building.
The structure that has become the Clifton Inn was built around 1799 by Thomas Mann Randolph, the son-in-law of Thomas Jefferson. During the American Civil War, the wife and children of famed Confederate cavalry leader John Singleton Mosby were sheltered at Clifton while Union troops drove them from their home near Middleburg and passed through the area.
The house remained a private residence in the hands of many owners until its current owners, T. Mitchell and Emily B. Willey, bought the property in 1983. They opened a five room bed and breakfast in 1985. Gradually, more buildings and additions added to this capacity. A restaurant also opened on the property in 1991.