Eric Chu Li-luan of the ruling Kuomintang (KMT, or the Chinese Nationalist Party) got only 30 percent of the vote and has already admitted defeat, according to the news outlet.
The victory of Tsai Ing-wen, who has pledged to maintain Taiwan’s status quo of de-facto independence, could lead to cooling in the relations between Beijing and Taipei.
Taiwan became self-governed in the 1940s after a civil war but China still considers it part of its territory.
The presidential election comes two months after a historic meeting between Chinese leader Xi Jinping and Taiwanese departing President Ma Ying-jeou.
In December, Director of the Chinese State Council’s Taiwan Affairs Office warned that China’s relations with Taiwan are headed toward "complicated changes" in 2016.