Family life was short lived for Fanny Chamberlain with the arrival of the American Civil War. Her husband took a leave of absence from Bowdoin (despite the college's protests) to join the Union war effort as lieutenant colonel of the 20th Maine Volunteer Infantry Regiment. Fanny remained at home raising their two small children, while he rose through the ranks. There is speculation that she resented the Army for disrupting her life, and her great fears of abandonment once again rose to the surface.