"It's the first time in 14 years that a Dutch foreign minister is visiting Iran," the ministry said in a statement saying Koenders' trip would take place on Sunday and Monday.
The Dutch diplomat is scheduled to meet his Iranian counterpart Mohammad Javad Zarif and Iranian President Hassan Rouhani for talks on trade links, implementing the nuclear deal, and other regional and international issues.
Koenders said he hoped to give "fresh impetus" to his country's ties with Iran and provide "greater opportunity to talk constructively with each other."
Koenders trip follows hot on the heels of other European ministers keen to restore ties with Tehran in the wake of the historic July nuclear accord struck between the Islamic Republic and the 5+1 group of countries.
French Foreign Minister Laurent Fabius, British Foreign Secretary Philip Hammond and EU Foreign Policy Chief Federica Mogherini as well as President Heinz Fischer and German Vice Chancellor Sigmar Gabriel have already travelled to Iran to improve bilateral relations with the Islamic Republic.