Several grist mills were established in what is now the neighborhood as early as 1640. Eli Whitney chose a mill at the base of East Rock, with water power from the Mill River, as the site of his gun factory in 1798, and built a boarding house for unmarried workers nearby, establishing the village of Whitneyville.
As shown in this map from 1868, Whitneyville originally centered at Whitney's armory. It later shifted to the Congregational Church near the center of the map.
In 1860 Whitney's son, Eli Whitney Jr., completely rebuilt the factory and increased the height of the mill dam. This provided more water power and created Lake Whitney, the first municipal water supply for New Haven. He was also a financial supporter of Whitneyville Congregational Church, almost a mile north of the factory, and the neighborhood center began to shift there. By 1900 the electric trolley line from New Haven reached Whitneyville, leading to the subdivision of surrounding land for residential development. The neighborhood street network was substantially complete by 1927.
Houses continued to be built well into the twentieth century, notably several distinctive modern homes on Deepwood Drive, and the last house in which playwright Thornton Wilder lived