A number of schools have served students of Whitesboro since the area was settled in the late nineteenth century. The first known schoolhouse in Whitesboro was a log structure built in 1785 near where the Whitesboro Town Hall now stands. A later brick schoolhouse stood near the former engine house on Mosely Street. The Whitestown (Whitesboro) Academy was a private school, founded in 1813 and was supported by private fees.
In 1827, the Oneida Institute aka the Oneida Academy was established and renamed the Whitestown Seminary in 1844. It was the first school in the country to admit African American students and was run for a time by the abolitionist, Beriah Green.
In 1858, a two story wooden building, formally incorporated as the Union Free School District of Whitesboro but known as the "Old Green School" to residents, was erected and it served as a school for 69 years. In 1919, the Main Street School was erected on the site of the "Old Green" school and served both elementary and high school students. It later became the grade school for kindergarten through sixth grade. This building survives today as apartments.
With an increase in population, a new high school was needed and the Whitesboro Central High School was erected on Oriskany Boulevard between 1936 and 1938. It currently serves as the Whitesboro Junior High today. The first Che Ga Quat Ka yearbook was issued in 1936.
On May 11, 1936, the school district became centralized and first known as the Whitesboro Central School District. The Whitesboro Central School District was reorganized in 1966 with the opening of the Marcy Senior High School in 1967. It serves as the Whitesboro Senior High School today for students in grades 9 - 12.