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The partnership in port operation has become an important concept in port development. Port operation is the main core activity in port business that strongly related to hight cost investment and technological equipment. Intermodal transport is one of the port operation activity to improve port efficiency and productivity in order to decrease congestion in the port. Private parties has a fundamental role in port development to cope with the lack of government budget by transfrering some of port development project and operating cost to the private parties. Port of Belawan has a lack of experience in public private partnership. In other hand, the Port of Rotterdam has a long experience in partnership implementation to upgrade the port operation through physical infrastructure and promoting intermodal transport. This research explores the partnership concept in port operation concerning intermodal transport and to know its implementation in both ports. There are four comparative analysis that are being used to analyze the implementation of the partnership in port operation: The first, policy and regulatory framework;second, public and private role in partnership; third, planning and development; and forth, inland transport connection and services. The result of this research concludes that the Port of Rotterdam is more flexible in contract agreement and promoting transperancy and accountability in public private partnership than Port of Belawan. Furthermore, this research recognize some lessons learned from the Port of Rotterdam that can be adopted in Port of Belawan, those are, encouragingpartnership by maintaining the investment climate, composition foreign ownership in port facilities, intermodal transport colaboration and Port Model and management.