Rev Canon Kevin Robertson says he is "overwhelmed" with the appointment.
Mr Robertson has two children with his partner Mohan and has been elected into the Diocese of Toronto alongside two other suffragan bishops.
He was first ordained in 1997.
The Diocese says that the 45-year-old was elected on the fourth ballot of the second election.
He said: "I didn't really expect to be standing here on the steps, but I'm deeply, deeply honoured.
"I realize this is an historic day in the life of our church.
"It's no secret that I'm the first openly gay, partnered bishop-elect in the diocese and perhaps in the Canadian church as well, and I know that for some people that's a real challenge and for others it's the fulfillment of what they've been hoping and praying for a very long time.
"The peace and unity of the church is really important to me and I will work to continue that peace and unity as a bishop."
Rev Canon Robertson was ordained in 1997.
The Anglican Church of Canada started accepting same-sex unions in 2002 before the country nationally legalised same-sex marriage in 2005.
There was a protest against the inclusion of, what the diocese said was "one candidate whose lifestyle is, to the best of my knowledge, irregular according to the teaching of the church regarding chastity and marriage," thought to be Kevin Robertson.
However Rev Canon Kevin Robertson said: "I absolutely see myself as a bishop for the whole church, including people who have a very different view of things than I do.
"I'm their bishop, too."
