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The city dates its founding to the period between 1831 and 1837, following the Indian Removal Act, when Erastus Gary laid claim to 790 acres (320 ha) of land near present-day Warrenville. The Wheaton brothers arrived from Connecticut, and in 1837, Warren L. Wheaton laid claim to 640 acres (260 ha) of land in the center of town. Jesse Wheaton later made claim to 300 acres (120 ha) of land just west of Warren's. It was not long before other settlers from New England joined them in the community. In 1848, they gave the Galena and Chicago Union Railroad three miles (5 km) of right-of-way, upon which railroad officials named the depot Wheaton. In 1850, ten blocks of land were platted and anyone who was willing to build immediately was granted free land. In 1853, the lots were surveyed and a formal plat for the community was filed with the county. The community was then incorporated as a village on February 24, 1859, with Warren serving as its first President. The village was later incorporated as a city on April 24, 1890, when the first mayor of the city was selected, Judge Elbert Gary, son of Erastus Gary and founder of Gary, Indiana.

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 on the Galena and Chicago Union 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, in 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.

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 the 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 of the last remaining records, which were then 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 for lunch during the vote when duplicate ballot stuffing allegedly occurred. 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.

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. 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 (230,000 m²) 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. 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.

Wheaton has rapidly expanded since the 1950s, although population growth has slowed since the early 1990s, as the city has become increasingly landlocked. Downtown lost much business after the county courthouse facility moved two miles (3 km) west in 1990, but in the decade since, the downtown has seen a renaissance of sorts, with the creation of several significant condominium and business developments. One of the most recognizable landmarks of the city is Wheaton Center, a 758-unit apartment complex on 14 acres (57,000 m²) in downtown Wheaton. The six building complex includes two twenty-story high-rise buildings built in 1975.

In 1887, Wheaton prohibited the sale of alcoholic beverages, a ban which lasted until 1985 and applied to all supermarkets, convenience stores, restaurants, and other establishments.

As of the census of 2000, there were 55,416 people, 19,377 households and 13,718 families residing in the city. The population density was 4,938.5 people per square mile (1,907/km²). There were 19,881 housing units at an average density of 1,771.7 per square mile (684.1/km²). The racial makeup of the city was 89.85% White, 4.85% Asian, 2.82% African American, 0.11% Native American, 0.02% Pacific Islander, 1.03% from other races, and 1.31% from two or more races. Hispanic or Latino people of any race were 3.65% of the population.

There were 19,377 households, of which 36.7% had children under the age of 18 living with them, 61.4% were married couples living together, 7.3% had a female householder with no husband present, and 29.2% were non-families. 24.5% of all households were made up of individuals, and 7.5% had someone living alone who was 65 years of age or older. The average household size was 2.64 and the average family size was 3.20.

In the city, the population was spread out, with 26.2% under the age of 18, 10.5% from 18 to 24, 28.8% from 25 to 44, 23.4% from 45 to 64, and 11.2% who were 65 years of age or older. The median age was 36 years. For every 100 females, there were 94.9 males. For every 100 females age 18 and over, there were 90.0 males.

According to the 2005–2009 American Community Survey, the median household income was $85,257, and the median family income was $107,763. Males had a median income of $81,515 versus $47,739 for females. The per capita income for the city was $41,353. About 3.3% of families and 4.8% of the population were below the poverty line, including 4.7% of those under the age of 18 and 7.4% of those ages 65 and older.

In August 2010, the city was listed among the "Top 25 Highest Earning Towns" on CNNMoney, purporting a median family income of $113,517, and a median home price of $328,866, based on 2009 figures.