The six Coral Triangle countries: Indonesia, Malaysia, Papua New Guinea, Philippines, Solomon Islands, and Timor-Leste, each have evolving systems of marine protected areas (MPAs) at the national and local levels. Now with more than 1,900 MPAs covering 208,152 km² (1.6% of the extended economic zone for the region), the Coral Triangle Initiative for Coral Reefs, Fisheries and Food Security has endorsed a Regional Plan of Action that contains a target of establishing a “Coral Triangle Marine Protected Area System” as part of its third goal on improving MPA management. This article details the contents of the Coral Triangle Marine Protected Area System Framework and Action Plan and describes its development and potential contribution to the improved management in the region once it is implemented. The MPA System Framework, as endorsed by the six countries, contains guidance for standardizing how MPAs and MPA networks are evaluated for effectiveness, and provides options for scaling-up existing MPAs to networks of MPAs that are more ecologically linked, integrated with fisheries management and responsive to changing climate. The Framework establishes an institutional mechanism by which the regional entity can facilitate the continued development and implementation of a region-wide MPA system that provides incentives for improved quality of management and enhanced marine area coverage at the local scale.