In 1857 the Illinois state legislature authorized an election to be held to decide the question of whether the DuPage county seat should remain in Naperville or be moved to the more centrally located Wheaton, which was also on the Chicago and Galena Railroad. Naperville won the election by a vote of 1,542 to 762. Hostility between the two towns continued for the next decade and another election was held in 1867, of which Wheaton narrowly won by a vote of 1,686 to 1,635. At a cost of $20,000, the City of Wheaton quickly built a courthouse to house a courtroom, county offices and a county jail.

The building was dedicated on July 4, 1868.[2] However, animosity between the two towns continued, and in 1868, as records were moved from the old Naperville courthouse to the new one in Wheaton, Naperville refused to turn over remaining county records, prompting a band of Civil War veterans from Wheaton to conduct what came to be known as the Midnight Raid on the Naperville courthouse. As Wheatonites fled back on Wheaton-Naperville Road, Napervillians were able to secure some last remaining records, which were taken to the Cook County Recorder in Chicago for safekeeping.

During this time, Naperville was mounting a lawsuit against Wheaton accusing election judges of leaving their posts during the vote. As the courts deliberated the fate of the county seat, the records were destroyed in the Great Chicago Fire of 1871. Shortly thereafter, Wheaton was officially proclaimed the county seat.[3] As demand for space increased, the courthouse was rebuilt in 1887 at a cost of $69,390, modeled after the courthouse in Aledo. This structure was used for the next 94 years until the county's rapid growth prompted the building of a brand new complex.[4] The old courthouse is listed on the National Register of Historic Places, and was formerly used by National-Louis University until National-Louis moved to Lisle in 2004.

It is currently being developed into luxury condominiums. On November 2, 1990, the courthouse moved to a building about two miles (3 km) west in a new 57 acre complex at the corner of County Farm Road and Manchester Road. It was built at a cost of $52,500,000 and includes a 300,000-square-foot (30,000 m2) judicial building. In 1992, the county sued the architect and contractor for $4 million after several employees became ill from the ventilation system.[5] In the end, however, the county received only $120,000 for minor repairs and the jury sided with the defendants, finding that the alleged problems were caused, primarily, by the county's negligent operation and maintenance of the ventilation system.