The agreement has been signed by President Ebrahim Raisi and will be sent to Parliament in the form of a bill to run its legal course.
The Raisi administration says it agreed to the bill given the need to put in place a judicial cooperation mechanism between Tehran and Brussels and to expand bilateral ties.
Belgian parliament has already approved the prisoner swap treaty with Iran, but a Belgian court put it on hold for the time being.
Under the deal, Iranian diplomat Assadollah Assadi who is under arrest in Belgium for allegedly orchestrating an attack against a gathering of the MKO terrorist group in Belgium will be exchanged with a Belgian national in custody in Iran for espionage.
Iran vehemently denies Assadi planned an attack on Belgian soil.