The agreement was signed by Iranian Justice Minister Mostafa Pourmohammadi and the Japanese envoy to Tehran on Sunday.
Pourmohammadi noted that the agreement is the second in kind which is signed between Tehran and Tokyo after 57 years.
He expressed the hope that the agreement would be endorsed by the two countries' parliaments in order to expedite the prisoners' swap process.
Iran has signed numerous prisoners swap deals and agreements on the extradition of criminals with different world states in the last decade.
Diplomatic relations between Iran and Japan were formally established in 1926 and throughout history, the two countries have maintained a friendly and strongly cooperation in various arenas.
The two countries' officials have held talks in different economic, trade, political and cultural fields in recent years to explore new ways of expanding bilateral ties.
Iran is one of the main oil suppliers to Japan.