In 1856 Maryland voters elected Purnell to statewide office as comptroller and he moved his family to Annapolis.

Although the units would continue to serve for three years (and many til the war's end), Purnell resigned from the military, holding the rank of colonel, in February 1862 and resumed the position of post master of Baltimore.

The infantry would then be assigned to Pope's Army of Virginia and later to the Army of the Potomac, and while held in reserve at the Second Battle of Bull Run, fight in the Maryland Campaign and Battle of Antietam, then the actions around Petersburg and Richmond, Virginia, before being amalgamated into the 1st Maryland Infantry at war's end.

[10] Purnell was a strong supporter of co-education[11] but after a fifteen-year trial, Delaware College stopped accepting female students by a vote of the board on June 24, 1885.

[13] Purnell than accepted the presidency of Hood College, a female seminary in Frederick, Maryland, and later of New Windsor College in Carroll County, Maryland, only to return to his alma mater in 1897 as an instructor in oratory, which position he held until his death.