It was built in 1905–1907 and was designed by McKim, Mead & White in the Neoclassical style; the building was part of the firm's original master plan for the campus.

[5][6][7][8] When Columbia became a university and relocated to Morningside Heights in the 1890s, there were originally no plans for the area south of 116th Street, where Hamilton Hall now sits, or for any facilities dedicated to the undergraduate college.

Two stained glass windows depicting Sophocles and Virgil, gifts from the class of 1885 and 1891, respectively, were installed in the Hamilton Hall lobby in 2003, having sat in storage for nearly 60 years.

Starting in the latter half of the 20th century, Hamilton Hall was taken over several times in the course of student activism at Columbia University, first during the protests of April 1968.

[15][16] In April of 2024, a group of students, staff, alumni, and allies unaffiliated with the school, who had been participating in a tent encampment protesting the Israel-Hamas war occupied the hall.