"The UK and the EU are important strategic partners for Canada with whom we enjoy deep historical ties and common values," the prime minister said in a statement.
"We will continue to build relations with both parties as they forge a new relationship."
Britain is Canada's third-largest trading partner after the United States and China, and Ottawa had supported Britain staying in the EU.
The former British colony is also seeking to finalize a free trade deal with the EU, signed in 2014.
Trudeau commented, "We are well positioned to weather global market uncertainty as we have done in the past.
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