Such passages typically upset China, which claims democratic and self-ruled Taiwan as part of Chinese territory.
In April, Beijing condemned a French decision to send a frigate through the strait as illegal, and China has also been upset by U.S. navy ships passing through the same waterway.
Canada's government said the frigate HMCS Ottawa passed through the Taiwan Strait on Monday and Tuesday.
"This route was chosen as it was the most direct route between UN Security Council sanctions monitoring activities in Northeast Asia and engagements in Southeast Asia," the Department of National Defence said.
"The Royal Canadian Navy does not conduct so-called Freedom of Navigation operations aimed at challenging the territorial claims of other nations, and the ship's transit was conducted in accordance with international law, including the United Nations Convention on the Law of Sea."
In June, two Canadian ships also sailed through the narrow strait that separates Taiwan from China, but denied that Canada was trying to make any kind of political point.
Taiwan's Defence Ministry said the latest ship passed through the strait in a southerly direction and was monitored throughout by Taiwan's armed forces.
There was no immediate reaction from Beijing.
Canada-China relations have nose-dived in the past year.
China, furious that Canadian police arrested a senior Huawei Technologies Co executive on Dec. 1 on a U.S. warrant, has blocked imports of meat products and canola seed from Canada and charged two Canadian men with spying.However both countries have recently appointed new ambassadors to each other's capitals, in a sign ties may be warming up.