Associated Press journalists watched as Rouhani, 68, registered Friday the fourth day of the registration period which ends on Saturday evening.
Running on the platform "More freedom and peace" Rouhani said, "Freedom should be expanded in both scope and strength in this country".
Iranian hard-liners had widely hope Raisi would challenge incumbent President Hassan Rouhani.
Some analysts doubt that Rouhani, who was elected in a landslide in 2013 on a pledge to reduce Iran's isolation and create a freer society, has enough will to improve the country's human rights situation.
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However, despite months of talks, hardliners have been unable to unite behind a single candidate.
Others believe Rouhani has depleted his political capital with the Supreme Leader by securing his consent to the 2015 nuclear deal, leaving nothing for domestic reforms.
Raisi also registered on Friday for the vote.
The Press TV article claimed that reformists lack a unified economic strategy, whereas principlists as a whole support large-scale privatization and opposing Iranian integration into a neo-liberal, globalist system that they see as benefiting only established world powers like the US.
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The next question is whether he will be approved by the conservative-controlled Guardian Council, who will vet the hundreds of registered hopefuls over the coming week, with the election due on May 19.
Earlier on Friday, President Hassan Rouhani applied for presidential candidacy.
Raisi, appointed by the Supreme Leader Ayatollah Ali Khamenei, is now the custodian and chairman of the Shrine of Shiite Imam Reza in the northeastern Iranian city of Mashhad.
A potential spoiler appeared on Wednesday, when former hardline president Mahmoud Ahmadinejad made the shock move of registering for the election against Khamenei s advice. The council normally does not approve dissidents or women. Rouhani registered on Friday with Iran's Interior Ministry, but all candidates in Iran's election - almost 900 so far - must be approved by the Guardian Council, which is expected to announce qualified candidates on April 27.
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