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With some 90% of the 28.6 million ballots counted, Raisi's tally was 17.8 million, interior ministry official Jamal Orfi said.
India has not chosen the new site yet, which could be controversial as the country has seen vehement protests against new nuclear sites.
Iran, which denies its nuclear programme is aimed at building a bomb, has gradually rolled back its commitments under the accord since the United States quit.
Iran has accused the three EU member states - Britain, France, and Germany - of inaction over sanctions the United States reimposed on it after unilaterally withdrawing from the landmark accord in 2018.
Iran threatened to do more - including enriching uranium to a higher level - if countries did not shield it from U.S. sanctions.
Iran's Supreme Leader Ayatollah Ali Khamenei set out last year a series of conditions for European powers if they wanted Tehran to stay in the nuclear deal, including continued purchases of Iranian oil.
Tensions began rising in May when the US rushed thousands of additional troops, an aircraft carrier, nuclear-capable B-52 bombers and advanced fighter jets to the Mideast.
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