Palo Alto County is named for the first battlefield victory in the Mexican War, which was fought on May 8, 1846.

The county was established in 1851.  The first settlement in the county was at West Bend. In 1857 some men of Palo Alto County joined the relief expedition from Fort Dodge to the scene of the Spirit Lake Massacre. (See Dickinson County.) West Bend provided food and shelter for both the military group and survivors of the massacre.

As soon as the county was organized on December 20, 1858, three locating commissioners met to locate the site of the county seat. The site they selected was a small village called Paoli, although county business was taken care of at a placed called Soda Bar.

County swamp land was sold to pay for the courthouse and a school in Paoli. The two-story brick structure collapsed during its construction. County officials decided to rebuild the building, this time only half the size. The courthouse was finally completed in 1859.

In 1874, representatives of a railroad company met with businessmen of Old Town, the most established community at the time, proposing a mass move. Having platted the new town, the railroad was willing to give businessmen choice lots if they would move. On September 2, the first business moved. By December, the town of Emmetsburg had come into existence, to become the county seat in 1875.

In 1880 a brick courthouse was built in Emmetsburg, which is named after the Irish patriot Robert Emmet. This 1880s building has undergone extensive repairs over the years. Originally faced with yellow brick, it was refaced with red brick during World War I. A tall tower was removed in the 1920s, and the jail was removed from the basement and relocated. It was extensively remodeled in 1970, and a two-story and basement addition was completed in 1976-1977.

Out front, on the courthouse lawn, stands a statue of Robert Emmet and a rock appropriately named the "Blarney Stone."