During the Civil War, Rebecca Littlepage found her home became the center of conflict between Confederate soldiers and pursuing Union troops. Confederate General Wise wanted to use the home as his headquarters, but Rebecca refused to allow this. Wise then threatened to destroy the home should Rebecca defy his authority, but she stood her ground. When ordered to fire upon the house, Confederate soldiers refused to do so as Rebecca and her children refused to leave the home. Rebecca saved the home from destruction, but the property was damaged as soldiers dismantled the outbuildings for firewood and either confiscated or consumed the farm's livestock.
In 1862, the Littlepage Mansion was the victim of misdirected bombardment by Union forces, but the house only sustained minor damage. Rebecca's husband, A. Littlepage, was killed while in Confederate service in April of 1862, leaving her a widow with seven children. Rebecca would eventually have to sell off some of the farm to pay taxes and support her family.