Noboa studied political and social sciences and is Doctor in Law from the Catholic University of Guayaquil. He was Chancellor of the University in 1986-1991 and 1991-1996.
Noboa was governor of Guayas Province from March 1983 to August 1984. In the 1998 presidential elections he was the running mate of Jamil Mahuad, who won. He was sworn in as Vice President of Ecuador on August 10, 1998.
On January 21, 2000, a military coup deposed Mahuad's government and the following day Noboa became President of Ecuador in constitutional order. He had the popular support of the country's indigenous people.
Noboa's presidency was marked by attempts to revive the Ecuadorian economy, which was in a recession at the time, including the freeing of US$400 million worth of assets frozen by the previous government. He left office in 2003 after Lucio Gutiérrez was victorious in the 2002 presidential election.
After his term ended, accusations of irregularities in foreign debt negotiation that cost the country $9 billion dollars were levelled at the former president. He completely denied the charges, which could have had him sent to jail for twenty five years if convicted. Claiming that he was the victim of unfair persecution, he applied for political asylum in the Dominican Republic, which was granted on August 11, 2003. The Supreme Court case against him was annulled by an unconstitutional, yet functioning, Supreme Court on the grounds that the case was not initiated by a two-thirds congressional vote as the Constitution stipulates. Shortly after, however, the presidency of Gutiérrez ended and the charges were reinstated. He was placed under house arrest in May 2005 and Ecuador's Interior Minister planned to prosecute. On March 16, 2006, a Supreme Court judge lifted the detention order and charged Noboa of being an accessory after the fact. Noboa said he would appeal this charge as well.