Saunders County was created by the Territorial Legislature on Jan. 26, 1856 and at that time was named Calhoun County. But the name Calhoun was not popular among early settlers in the territory, as a government surveyor by that name was suspected of corruption and graft. So in 1862 the Territorial Legislature changed the county's name to Saunders, in honor of territorial Gov. Alvin Saunders.

Ashland is believed to be the first settlement in the county. For many years the area stretching north along the Platte River from Ashland to Leshara was home to the Otoe Indians, while the Pawnee Indians were camped in the bluffs in the northern part of the county.

When the first county election was held in 1866, the settlement of Ashland was chosen as the county seat. In 1870 the county's first courthouse would be built here. Ashland's status as home to this new county's government would be short-lived, however, as in 1873 voters chose a more centrally located Wahoo. Within a year a courthouse would be built in the new county seat and stand for the next 30 years. By the beginning of the 20th century the county was in need of a new home for its offices and in 1904 the present courthouse was built at a cost of $87,000.

Located on the east lawn of the courthouse today is a replica of a Mark 14 torpedo, which stands as a memorial to the U.S.S. Wahoo and its crew of 65 who perished during World War II. The submarine was credited with sinking 20 Japanese ships before it was sunk by enemy action on Oct. 11, 1943. Each October a memorial service is held at the courthouse to honor those who gave their lives in submarine warfare.

A frequently-asked question is how the county seat received its unique name. There are actually two versions that are used to provide the answer. The first is that the name originates from an Indian word for a medicinal plant known as the "burning bush," which grew along the banks of the Wahoo Creek. The second explanation is the name is from the word "pahoo," which means "not very bluffy" terrain.