Dr. Budhendra Doobay emigrated to Canada from Guyana in 1972 and quickly noticed the spiritual vacuum felt by the Indo-Caribbean Hindu community, who had maintained faith through three generations of Caribbean indenture and now found themselves in a new country. In 1980 he purchased a small residential property on Yonge Street in Richmond Hill and began conducting weekly Sabha services in his own home; within a year attendance had outgrown the house, and in 1981 a simple wooden mandir was built on the site.

The mandir grew organically through the 1980s and 1990s as the Indo-Caribbean community in the GTA grew from a few hundred families to over 100,000. In 2002 the original wooden mandir was replaced with the current stone-and-concrete temple, consecrated by pandits from India and Guyana. The Canadian Museum of Hindu Civilization opened in 2005 with support from the Government of Ontario.

In 2010 Dr. Doobay commissioned one of the most ambitious Hindu art projects in Canadian history: a 50-foot outdoor Hanuman murti, the tallest outside India at the time. Designed by Indian sculptors and constructed from steel-reinforced concrete with fibreglass outer layer finished in weather-resistant saffron, the murti was unveiled at a public Pran Pratishtha ceremony attended by 10,000 devotees and the Premier of Ontario. The statue is now a mandatory pilgrimage point for Hanuman devotees across North America, particularly on Hanuman Jayanti when up to 20,000 devotees visit.

Vishnu Mandir has expanded further with a Yog Shala, a classical music academy, a Sanskrit school, and a Hindu community food bank distributing over 200,000 meals annually. A major renovation in 2019 added the Atmavidya Hall for youth programming, and in 2023 the mandir celebrated 42 years of continuous service with a commemorative plaque from Parliament Hill.