In high school Erdoğan became known as a fiery orator in the cause of political Islam. He later played on a professional football (soccer) team and attended Marmara University. During this time he met Necmettin Erbakan (Erbakan, Necmettin), a veteran Islamist politician, and Erdoğan became active in parties led by Erbakan, despite a ban in Turkey on religiously based political parties. In 1994 Erdoğan was elected mayor of Istanbul on the ticket of the Welfare Party. The election of the first-ever Islamist to the mayoralty shook the secularist establishment, but Erdoğan proved to be a competent and canny manager. He yielded to protests against the building of a mosque in the city's central square but banned the sale of alcoholic beverages in city-owned cafés. In 1998 he was convicted for inciting religious hatred after reciting a poem that compared mosques to barracks, minarets to bayonets, and the faithful to an army. Sentenced to 10 months in prison, Erdoğan resigned as mayor.

After serving four months of his sentence, Erdoğan was released from prison in 1999, and he reentered politics. When Erbakan's Virtue Party was banned in 2001, Erdoğan broke with Erbakan and helped form the Justice and Development Party (Adalet ve Kalkınma Partisi; AKP). His party won the parliamentary elections in 2002, but Erdoğan was legally barred from serving in parliament or as prime minister because of his 1998 conviction. A constitutional amendment in December 2002, however, effectively removed Erdoğan's disqualification. On March 9, 2003, he won a by-election and days later was asked by President Ahmet Necdet Sezer to form a new government. Erdoğan took office on May 14, 2003.

As prime minister, Erdoğan toured the United States and Europe in order to dispel any fears that he held anti-Western biases and to advance Turkey's bid to join the European Union. Although the previous government had refused to allow U.S. troops to be stationed in Turkey during the Iraq War, in October 2003 Erdoğan secured approval for the dispatch of Turkish troops to help keep the peace in Iraq; Iraqi opposition to the plan, however, prevented such a deployment. In 2004 he sought to resolve the issue of Cyprus, which had been partitioned into Greek and Turkish sectors since a 1974 civil war. Erdoğan supported a United Nations plan for the reunification of the island; in April 2004, Turkish Cypriots approved the referendum, but their Greek counterparts rejected it. Tensions between Turkey's secularist parties and Erdoğan's AKP were highlighted in 2007, when attempts to elect an AKP candidate with Islamist roots to the country's presidency were blocked in parliament by an opposition boycott. Erdoğan called for early parliamentary elections, and his party won a decisive victory at the polls in July.

In early 2008 parliament passed an amendment that lifted a ban on the wearing of head scarves—a sign of religion long contested in Turkey—on university campuses. Opponents of the AKP renewed their charges that the party posed a threat to Turkish secular order, and Erdoğan's position appeared to come under increasing threat. In March the constitutional court voted to hear a case that called for the dismantling of the AKP and banning Erdoğan and dozens of other party members from political life for five years. Erdoğan successfully maintained his position, however, when in July 2008 the court ruled narrowly against the party's closure and sharply reduced its state funding instead.