Pachakutik participated in the presidential elections of 1996 despite having only been formed a few months beforehand. In order to give a strong media boost to the party in their first presidential election, they recruited a former TV personality named Freddy Ehlers to represent the party on the highest national stage. Although Ehlers failed to win the election, he placed third with nearly twenty percent of the popular vote despite having less than five months to prepare his campaign. In addition, eight members of Pachakutik won seats as national deputies, including CONAIE president Luis Macas, and although they constituted less than ten percent of the seats in the National Congress of Ecuador, the presence of the party was undeniable. For the first time indigenous citizens of Ecuador were present in Congress, representing the interests of all groups throughout the country.
Pachakutik, along with a strong civil society effort by CONAIE and others, was instrumental in pushing for the new Ecuadorian Constitution in 1998 which, among other things, recognized the country as multi-cultural, paving the way for such reforms as bilingual education. Since the 1998 elections in which Pachakutik’s amount of representation declined, the party has never quite reached its prior levels of support and has been unable to topple the majority of the Congress that does not share their views. It has been criticized by CONAIE for its ineffectiveness, leading to a coup d'état in 2000 organized by CONAIE in association with sympathetic members of the military. Although after only hours of taking the capital and instituting a three-man junta including CONAIE president Antonio Vargas the government dissipated, echoing CONAIE’s frustration. Pachakutik has since distanced itself somewhat from CONAIE while still remaining intensely involved with gaining indigenous rights.
At the 2002 legislative elections, the party won at least 11 out of 100 seats. Its candidate Lucio Gutiérrez, member of the Patriotic Society Party 21 January won 20.3% of the vote in the presidential elections of the same day and won the second round with 58.7%.
After three months of government Gutierrez broke up its alliance with Pachakutik and he discharged its ministers. The party soon grew to despise him and publicly criticize him. In 2003 they even began to call for the removal of President Gutiérrez publicly in the media. The political party is struggling with problems of identity at this point in time and is in risk of losing all that it had originally gained in 1996.
However, with Gutierrez out, the return of Luis Macas to the presidency of CONAIE and the opposition to the signature of an agreement of free trade with United States, they have been able to reunify to the movement.
At the 2009 elections, the party had its worst results since its founding, but still maintains representation, with 4 seats out of 124 in National Assembly.