The 1860s
Upon the close of the 1850s, the Brookeville Academy entered a period of greater support and stability only to be disrupted once more. This time, however, the disruption was caused by the Civil War. Troops passing through Brookeville in 1862 and 1863 forced a drop in the number of boarding pupils. The Minutes do not adequately reflect the Civil War period since Reverend Orlando Hutton, Secretary of the Board, kept the records and they were never united with the other Minutes.

During the 1860s, several Trustees resigned-Reverend Orlando Hutton (1864), Remus Riggs (1867), and William K. Boyle (1868). Also in 1865, B. Worthington Waters and Enoch B. Hutton died. The vacancies were filled by William K. Boyle (1867), Thomas J. Holland (1865), Dr. James S. Martin (1867), Z. D. Waters (1867), and Thomas D. Riggs (1868).

E. B. Prettyman remained as Principal until 1864. He was followed by R. K. Burns who resigned when the Board felt that for the welfare of the school a change in Principals was in order (1865). The next Principal was Isaac Dunlin Parkinson, a graduate of Jesus College, Cambridge (1865).

Around the middle of the decade, the Board decided that the Academy needed more space. They pursued an option of purchasing a lot next to the boarding house owned by Owen J. Edmonston (1865); however, they chose Mr. Parkinson's plan in which he proposed the purchase of the Weer farm just outside of Brookeville.