Khatami, earlier in Paris for a two-day visit, had praised the pope for his efforts to promote 'coexistence, moderation and dialogue between religions'.
The Iranian president called John Paul II as 'someone who sought dialogue between Islam and Christianity', expressing his 'very great pleasure and honor' to participate at the funeral.
The funeral will be held in the Vatican at 10:00 am (0800 GMT) on Friday.
Khatami, heading a high-ranking delegation, arrived in Paris from Vienna late Monday. He met with his French counterpart President Jacques Chirac on Tuesday afternoon.
During his two-day stay in Paris, Khatami delivered a speech during the Conference on Dialogue Among Civilizations held at the premises of the United Nation Educational, Scientific and Cultural Organization (UNESCO).
While in Paris, he also conferred with French Interior Minister Dominique de Villepin, Algerian President Abdelaziz Bouteflika, and Secretary General of the Organization of the Islamic Conference (OIC) Akmaleddin Ehsan Uglu.
It was Khatami's second trip to France since taking office in 1997.
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