Winona's first settlers built a farming hamlet called "the Fifty" close to the creek of that name and tight to the waterfront. Winona's centre shifted in the late 19th century away from the water and the creek to a new central place built around the railway and roads, and tied together by Winona (then called Station) Road. Later, the focus shifted in favour of Highway 8, the escarpment, and Winona Road.
Winona was part of the township of Saltfleet. On January 1, 1974, it became part of the New Town of Stoney Creek. Stoney Creek became a city in 1985. Fifteen years later, it was forcibly merged with the City of Hamilton by order of the Ontario government.