This research aimed to know the influence of accessibility and cargo transport regulations on the operational performance mediated by logistics effectiveness in the Class II Port of Jayapura, Papua Province. Several main problems in the object of this research were the existence of operational hour limitation regulation which made cargo delivery not maximally run, limited road network and roads in the port area, as well as the occurrence of congestion if cargo ships and passenger ships arrived at the port at the same time. This research used Structural Equation Modelling with Smart3PLS-SEM. The sampling technique used probability sampling and was conducted in the Port of Jayapura. The respondents were as many as 250 people consisting of shipping business players, transportation service providers, Harbormaster’s office, and the Port Authority. The result of the analysis and discussion indicated that logistics effectiveness was a reinforcing factor in the achievement of port operational performance. The existing obstacles could be overcome through road infrastructure improvement, traffic engineering, continuous policy improvement, and port facility and infrastructure improvement. The key finding was the necessity of an information technology system used for the ship's loading and unloading activities digitally to be utilized by the stakeholders, shipping companies, stevedoring companies, expedition companies, and cargo owners.