Presidential elections were held in Taiwan on 18 March 2000 to elect the president and vice president. With a voter turnout of 83%, Chen Shui-bian and Annette Lu of the Democratic Progressive Party (DPP) were elected president and vice president respectively with a slight plurality.

This election ended more than half a century of Kuomintang (KMT) rule on the island, during which it had governed as a one-party state since the retreat of the government from the Chinese mainland during the closing stages of the Chinese Civil War in 1949. This was also the first time in Chinese history that a ruling political party peacefully transferred power to an opposition party under a democratic system. The nominees included the then-current vice president Lien Chan for the KMT, former provincial governor James Soong as an independent candidate (upon his loss of the KMT nomination), and former Taipei mayor Chen Shui-bian for the DPP.

Controversy arose throughout the course of the election; in particular, the candidacy of James Soong was beset by accusations of splitting the Kuomintang vote and involvement in corruption during the presidency of Lee Teng-hui, culminating in protests and the expulsion of the latter from the Kuomintang, while Chen's campaign attracted criticism from neighboring China due to his party's traditionally pro-independence stance. The issues of corruption and cross-strait relations were dominant during this election. Chen's victory was initially seen as unlikely, but several compounded effects like the splitting of the Kuomintang vote and the aforementioned controversies are seen as having led to his victory. Chen performed most strongly in the southern part of Taiwan, while Soong tended to win in northern areas.

The ruling Kuomintang (KMT) ran vice president Lien Chan for president and Premier Vincent Siew for vice president. Both were career civil servants and Lien, originating from the Taiwanese elite, was seen as aloof and unable to empathize with the common people.

Though more popular and consistently ranked higher in the polls, the outspoken former Taiwan governor James Soong failed to gain the Kuomintang's nomination. As a result, he announced his candidacy as an independent candidate. The Kuomintang responded by expelling Soong in November 1999. It is a very common belief among KMT supporters that president Lee Teng-hui was secretly supporting Chen Shui-bian, and purposely supported the less popular Lien in order to split the Kuomintang, and this belief was given a great deal of credibility after the 2000 election with Lee's defection to the Pan-Green coalition, though Lee's defection came only after his expulsion by the KMT. Soong, a mainlander, tried to appeal to the native Taiwanese by nominating surgeon Chang Chao-hsiung, who is a native Taiwanese, as his running-mate. This, combined with the fact that Chang had connections to both the Democratic Progressive Party and the KMT reinforced Soong's campaign message of bridging political and cultural divide.

In December 1999 the KMT began to attack Soong's integrity. They sued Soong for theft, alleging that as party secretary-general, he stole millions of Taiwan dollars in cash intended for the family of the late president Chiang Ching-kuo and hid the money in the Chunghsing Bills Finance Co. Soong defended himself by saying he was acting under Lee's direction, though Lee denied this and many found the explanation unconvincing. Initially holding a commanding lead in the polls, Soong ended up losing by just over 300,000 votes.

Both candidates had some obstacles presenting themselves as reform candidates with regard to corruption, given their high rank in the Kuomintang government. Soong's strategy was to openly admit his past wrongdoing and present his insider status as an advantage: i.e. that he could most easily tackle the corruption because of his experience with it; however, many saw his credibility as a reformer as broken by his financial scandal. Lien advocated for reform, but had some difficulty in direct criticism as such attacks may have offended the ruling government; this is thought to have contributed to his defeat.

The DPP ran former Taipei mayor Chen Shui-bian and Taoyuan County magistrate Annette Lu for vice president. Having run for the 1996 election on a radical independence platform and lost by a landslide, the DPP in May 1999 moderated its stance by issuing the "Resolution on the Future of Taiwan". The resolution accepted the status quo and promoted the moderate view that Taiwan was already independent, so any formal declaration would not be urgently necessary, if at all, and Chen presented a more conciliatory stance regarding the mainland. Also included was the pledge that any change in Taiwan's international status will have to be done through a referendum, thus alleviating the fear that, if elected, a DPP government would unilaterally declare independence without popular approval. The Chen-Lu ticket also promised to be more aggressive in fighting black gold, a system of connections and corruption which had become intertwined with the KMT. The last minute public endorsement of Chen Shui-bian by President of the Academia Sinica and Nobel laureate Yuan T. Lee is also thought to have played a role in his election, with Yuan T. Lee offering to negotiate with the PRC on Taiwan's behalf.