John Scott was born to John and Eliza (Skelly) Scott on April 14, 1824. He began teaching school in 1840 and used the money he earned to attend Franklin College in New Athens, Ohio. Scott moved to Louisville, Kentucky in 1845, where he taught school until the Mexican War broke out. He enlisted in the First Regiment of Kentucky Volunteers and performed scouting duties in Mexico until he was captured. Scott served three months in Santiago Prison and later published an account of his captivity,Encarceration, or the Prisons in Mexico, at the request of his comrades.

After his release, Scott returned to Kentucky and married Selina A. Bell of Orange County, New York. The couple had two children, Jessie and Ben Bell (1851-1886). John Scott taught at the Bath Seminary in Owingsville, Kentucky and published the Kentucky Whig until his wife's death on August 1, 1854. He settled in Nevada, Iowa in 1856 and married Annie Crabb (d. 1862) on January 18, 1858. The couple had two children, Carrie (d. 1878) and Rankin (1859-1869). After Annie Scott's death, John Scott married Mary Sophia Wright on November 24, 1863, and the couple had one daughter, Mary Avis (Scott) Jacks (1866-), who survived to adulthood.

John Scott was also active in politics and was elected to the Iowa State Senate in 1859. He temporarily abandoned this career in 1861 when he enlisted as the Captain of Company E of the 3rd Iowa Infantry Regiment. He was later promoted to Lieutenant Colonel, transferred to the 32nd Iowa Infantry Regiment, and promoted to Colonel. He left the Army in May of 1864 and returned to his political career, serving as the Lieutenant Governor of Iowa (1867-1869), Assessor of Internal Revenue for the Sixth Collection District, and State Senator. John Scott died in Des Moines, Iowa on September 23, 1903.