Henry Harnden was born March 4, 1823, in Wilmington, Massachusetts, to Jonathan Harnden and Rhoda Abbott. His father was a farmer who owned $820 of real estate in 1850. He attended school there but left at 18 to work as a deckhand on a ship. He spent the next five years travelling the world, visiting Africa and Central and South America. He returned home in the late 1840s and worked as a clerk in Lowell, Massachusetts. He married Mary Ann Leightner in Roxbury, Massachusetts, on December 27, 1847, and they had at least four children: Laura, born around 1849; Mary Jane, born around 1853; Rhoda, born around 1859; and Flora, born around 1861.
Harnden travelled to California in 1850 to take part in the gold rush. He returned to Massachusetts soon afterwards, and the family settled in Wisconsin around 1852. He briefly worked as a farmer before establishing a lumbering business. He enlisted in the Union army in the summer of 1861 as a private in a cavalry battalion. That fall, the army expanded the battalion into the 1st Wisconsin Cavalry, and Harnden was promoted to sergeant and then captain. Harnden took part in the Battle of Chickamauga and the Atlanta Campaign. He was promoted to major in 1864 and then to lieutenant colonel in January 1865. He mustered out on July 19, 1865, and returned home to Wisconsin.
He served in the Wisconsin legislature in 1866. He served as U.S. Assessor from 1867 to 1873 and then as U.S. Collector of Internal Revenue from 1873 to 1883. He died in Madison, Wisconsin, on March 17, 1900.