Allegations regarding Rouhani's plagiarism were first raised in 2013 when it was claimed that he had probably "lifted" sentences from a book by Afghan author Mohammad Hashim Kamali. Glasgow Caledonian University, Rouhani's graduation school, argued that the sentences were both cited properly. The issue was raised again amid 2017 Iranian presidential election when a student campaign claimed that they had for the first time investigated Rouhani's whole thesis using plagiarism detection tool iThenticate and that chapters one through four of Rouhani's thesis had been plagiarized at least 39%, 43%, 40% and 82%, respectively. Ayatollah Ali Akbar Kalantari, a member of the Assembly of Experts, Shiraz University faculty member and one of the alleged victims, said that "major segments" of Chapter 4 of Rouhani's thesis had been translated from his book without being referenced.
Rouhani was considered a leading candidate in the June election because of his centrist views yet close ties to Iran's ruling clerics and the Green Movement. He announced his presidential candidacy on 11 March 2013 and registered as a presidential candidate on 7 May. Amid the run-up to the election, former presidents Mohammad Khatami and Akbar Hashemi Rafsanjani, together with reformists supported Rouhani on the presidential race after pro-reform candidate Mohammad Reza Aref dropped out of the presidential race after Khatami advised him to quit in favor of Rouhani. On 10 June, Mehr news agency and Fars news agency, suggested that Rouhani might be disqualified prior to the election and The Washington Post, in an editorial, predicted that Rouhani "will not be allowed to win". On 15 June 2013, Interior Minister Mostafa Mohammad Najjar announced the results of the election, with a total number of 36,704,156 ballots cast; Rouhani won 18,613,329 votes, while his main rival Mohammad Bagher Ghalibaf secured 6,077,292 votes. Rouhani performed well with both the middle class and youth, even garnering majority support in religious cities such as Mashhad and Qom (an important seat of Shia Islam and the clergy, many of whom surprisingly do not support conservatives) as well as small towns and villages. Rouhani's electoral landslide victory was widely seen as the result of the Green Movement from the 2009 elections, with crowds chanting pro-reform slogans. Religious Iranians equally celebrated Rouhani's victory, demonstrating what analysts described as a thorough rejection of the policies of the conservative factions.
He was announced the winner on the day following the election. He received his presidential precept from his predecessor, Mahmoud Ahmadinejad on 3 August 2013 and entered Sa'dabad Palace in a private ceremony. His work as president officially began on the same day at 17:00 IRDT. He was inaugurated as the seventh president of Iran on 4 August in House of the Parliament.
Rouhani announced his cabinet on 4 August. He had a ten-day mandate for introducing his cabinet members to the parliament but he did not use this. Then, parliament voted on his cabinet, which was scheduled on 14–19 August. Between three reformist politicians (Mohammad Reza Aref, Eshaq Jahangiri or Mohammad Shariatmadari) that were likely for the vice presidency, Rouhani appointed Jahangiri for the position. There were also many candidates for the ministry of foreign affairs: Ali Akbar Salehi, Kamal Kharazi, Sadegh Kharazi, Mohammad Javad Zarif and Mahmoud Vaezi but Zarif became Rouhani's final nominee. Although several names were being circulated for the other ministerial posts before the final announcement, the office of president-elect denied these speculations. On 23 July 2013, it was reported that eight members of Rouhani's cabinet had been finalized: Jahangiri as first vice president, Zarif as foreign minister, Rahmani Fazli as interior minister, Tayebnia as finance minister, Dehghan as defense minister, Namdar Zanganeh as petroleum minister, Najafi as education minister, Chitchian as energy minister, Nematzadeh as industries minister, Hassan Hashemi as health minister and Akhondi as transportation minister. This become official after Rouhani presented the list of his ministry nominates to the parliament on his inauguration day. He also appointed Mohammad Nahavandian as his chief of staff.
According to a March 2014 report by Center for International Media Assistance, since Rouhani takeover in 2013, "Censorship of the Internet has only gotten worse, but it's more and more clear that Rouhani does not have complete control over this process".
In September 2013, eleven political prisoners were freed including noted human rights lawyer Nasrin Sotoudeh and Mohsen Aminzadeh. The move came just days before his visit to the United States for the United Nations General Assembly.
Rouhani's visit to New York City in September 2013 was hailed as major progress in Iran's relations with the United States. He previously said that his government is ready to hold talks with the United States after thirty-two years. Rouhani denied reports that during his trip he had refused a meeting with U.S. President Barack Obama, and felt more time was needed to coordinate such a meeting. On 27 September 2013, a day after the two countries foreign ministers met during the P5+1 and Iran talks, Rouhani had a phone call with President Obama that marked two countries' highest political exchange since 1979. However, due to this phone call Rouhani was protested by conservatives who chanted "death to America" when he returned to Tehran.
Rouhani began his presidency in November 2013 with approval and disapproval ratings near 58% and 27% respectively, according to Information and Public Opinion Solutions LLC (iPOS) which is assessing it on a quarterly basis. It gradually fell down to 48% and he recorded a 33% disapproval rating in May 2015. His job approval boosted after Joint Comprehensive Plan of Action, according to the survey conducted by IranPoll for the University of Maryland's Center for International and Security Studies (CISSM), standing on 88% with a large majority (61%) expressing a "very favorable view" of him (up from 51% in July 2014) and a ±3.2 margin of sampling error. The poll also indicated Rouhani has a "tough challenge" in maintaining the support due to the fact that people have high economic expectations from the deal, and it could become his Achilles' heel. iPOS has recorded a 54% approval and 24% disapproval, days after the deal in August 2015. The trend has continued until February 2016, with 67% and 18% approval and disapproval ratings, marking the highest level since he took office.