The town, at one time known as Bolton Mills Cemetery, was founded in around 1822 when James Bolton helped build a flour mill on a Native burial ground for his relative George Bolton.

By 1857, Bolton was a village with a population of 700 in the Township of Albion County Peel. It was settled on the River Humber on the line of the proposed Toronto Grey and Bruce Railway.

Bolton Camp was founded in 1922 by the Toronto Star newspaper’s first publisher, Joseph Atkinson, who wanted to provide a convenience for under-privileged children to escape the city. The camp was set on the site of an abandoned fishing club about 5km east of Bolton on King Street. Over its days thousands of children and adults called the camp home during the summer months.

The suburban housing developments began near King Street, up to 15th Sideroad of Albion (now known as Bolton Heights Road). The urban area did not expand until the late 1970s and early 1980s, which also led to advancement of an industrial area in the southwest. The urban area up to Columbia Way - the northern boundary - began growing in the late 1980s. Housing expansion continued towards the southern and the western parts of the town about 1 km northwest of the heart of town in the 1990s and the 15th Sideroad in about 1995, especially to the north.

The industrial area began adding buildings to the southwest up to Simpson Road. The urban areas merged with the southern part in 2000 and the northwest.