Abe, the prime minister of Iran's friendly country, will be welcomed by Iranian Foreign Minister Mohammad Javad Zarif at Mehrabad Airport.
Formal welcoming ceremony will be held by President Hassan Rouhani at Sa'dabad Complex.
Earlier, Iranian government spokesman Ali Rabie announced that Shinzo Abe is scheduled to hold meeting with Supreme Leader of the Islamic Revolution Ayatollah Seyyed Ali Khamenei.
The trip is to be made within the framework of traditional and longstanding relations and in line with developing bilateral ties and issues of mutual interest, he said.
Abe's visit to Tehran will be the first visit to Iran by a Japanese leader over past four decades after victory of the Islamic Revolution.
The Japanese Foreign Minister Tarō Kōno is also to hold talks with Zarif on Wednesday.
According to Japanese officials, Abe will not be able to be a mediator but his visit is aimed at reducing tensions and help restore stability in the Middle East.
The US president unilaterally withdrew from a multilateral nuclear deal with Iran on May 8, 2018, re-imposing two rounds of sanctions on the country the second of which targeted Tehran's oil exports.
After waging full-scale economic war against Iran, US president Donald Trump appealed to Prime Minister Shinzo Abe to mediate between Tehran and Washington.
Iran announced that it would suspend some of its commitments under the deal in reaction to the US hostile measures and would proceed with the trend after 60-day moratorium it gave to the European Union, Russia, China and Germany, the states parties to the JCPOA.
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