The village began to be settled in 1784, and was incorporated in 1813. An 1851 list gave the name Che-ga-quat-ka for Whitesboro in a language of the Iroquois people. The abolitionist Oneida Institute was located in Whitesboro from 1827 to 1843. of Whitesboro from 1891 with list of landmarks The older part of the village was bordered by the Erie Canal and the village's Main Street. When the canal was filled in the first half of the 20th century, Oriskany Boulevard was built over the filled-in canal. The streets that connect the two roads form the oldest part of the village. The Whitestown Town Hall was listed on the National Register of Historic Places in 1973.
The Whitesboro seal, originating in the early 1900s, displays founder Hugh White wrestling an Oneida Native American. The seal has been controversial because it has been interpreted as a settler choking the Native American; city officials contend it depicts a friendly wrestling match that White won, gaining the respect of the Oneida. The current version of the seal was created in 1970, after a lawsuit by a Native American group: the version used before the suit showed the settler's hands on the Native American's neck instead of his shoulders. The seal attracted more controversy in 2016 when village residents voted 157 to 55 to keep the seal as-is rather than explore alternative images. On January 21, 2016, Patrick O'Connor, the mayor of Whitesboro, called Jessica Williams, a correspondent for The Daily Show, and told her that the town would change the seal. An updated seal was adopted in the summer of 2017. The new seal was created by Marina Richmond, a student at the PrattMWP College of Art and Design in Utica. While the new seal depicts the same scene as the previous seal it has been changed so that it no longer depicts the Native American as being strangled. Additionally, inaccuracies like the design of the headdress worn by the Oneida chief have been corrected as well as the attire of Hugh White. The skin tone of the Oneida chief has also been whitened.
As of the census of 2000, there were 3,943 people, 1,778 households, and 992 families residing in the village. The population density was 3,675.4 people per square mile. There were 1,921 housing units at an average density of 1,790.6 per square mile. The racial makeup of the village was 97.69% White, 0.53% African American, 0.03% Native American, 0.33% Asian, 0.53% from other races, and 0.89% from two or more races. Hispanic or Latino of any race were 1.47% of the population. There were 1,778 households out of which 27.3% had children under the age of 18 living with them, 36.9% were married couples living together, 15.0% had a female householder with no husband present, and 44.2% were non-families. 39.0% of all households were made up of individuals and 18.7% had someone living alone who were 65 years of age or older. The average household size was 2.21 and the average family size was 2.98. In the village, the population was spread out with 23.3% under the age of 18, 7.8% from 18 to 24, 31.7% from 25 to 44, 20.3% from 45 to 64, and 17.0% who were 65 years of age or older. The median age was 37 years. For every 100 females, there were 86.7 males. For every 100 females age 18 and over, there were 81.2 males. The median income for a household in the village was $31,947, and the median income for a family was $42,741. Males had a median income of $29,408 versus $25,865 for females. The per capita income for the village was $17,386.
