During the summer of 1863, just after the Battle of Vicksburg, Thomas was among the volunteers who brought supplies to Indiana soldiers serving at Vicksburg, Mississippi. She returned north aboard a steamboat with 200 sick and wounded soldiers including 47 of them who were under her direct care. In addition to her service at Vicksburg, Thomas nursed wounded soldiers at hospitals in Washington, D.C.; Nashville, Tennessee; and Natchez, Mississippi. In 1864, Thomas was appointed superintendent and served for eight months at a hospital for war refugees and freed slaves in Nashville as assistant physician with her husband, who was the hospital's surgeon. Two of the Thomases daughters, Paulina and Julia, served as teachers for the refugees. After the Civil War, Thomas and her husband returned to Richmond, Indiana, where they continued their social activism.