The signed understanding would allow ships from both the countries to pass more easily through each others’ territorial waters and would help them get equal support in case of emergencies, Korea's Ministry of Oceans and Fisheries said on Tuesday.
Seoul and Tehran had unsuccessfully tried to implement a similar pact in 1998.
South Korea's export of fishery goods to Iran was estimated at US$21 million last year, which is equal to just 1 percent of the combined fishery export made by Asia's fourth-largest economy, Seoul-based Yonhap News Agency reported.
The new pact comes into force after economic sanctions against Iran have been lifted, and industry watchers expect Tehran to come up with more maritime projects to improvise its natural resources.
The Korean Register of Shipping, a non-profit ship classification society, and its Iranian counterpart also agreed to establish a joint venture to promote plant and engineering projects.
The ministry said the joint venture will allow South Korean firms to tap the Iranian market further.