He first ran for president in the September 1996 election, following the military coup of 1994. Running as the candidate of his newly formed United Democratic Party, Darboe finished second to incumbent Yahya Jammeh of the Alliance for Patriotic Reorientation and Construction (APRC) party, winning 35.84% of the vote compared to Jammeh's 55.77%. The election was roundly criticized by local and international observers as flawed.
Darboe's second attempt to gain the presidency came in October 2001. This time, he represented a three party coalition of his UDP, the People's Progressive Party (PPP), and the Gambian People's Party (GPP). Out of the five-candidate field, he again finished second behind Jammeh, receiving 32.59% of the vote. Unlike the 1996 vote, most observers endorsed the conduct and outcome of the poll.
In 2005, the UDP joined with four other opposition parties to form the National Alliance for Democracy and Development (NADD), in preparation for elections in late 2006 and early 2007. The alliance, however, disintegrated after the UDP and the National Reconciliation Party (NRP) withdrew in early 2006.
By the time presidential elections were held on 22 September 2006, Darboe's UDP had formed another coalition with the NRP and the Gambia Party for Democracy and Progress (GPDP) known as the "Alliance for Regime Change". Jammeh won the election with 67.33% of the vote followed by Darboe, who won 26.69%. A third candidate representing the remaining NADD parties, Halifa Sallah, finished a distant third with 5.98% of the vote.