This work uses the environmental contour line approach to estimate the long-term extremes of carbon emission generated by a bulk carrier operating in different sea state conditions, utilising short-term analyses of the ship propulsion energy efficiency as a function of hull resistance in calm water due to appendages, aerodynamic resistance, and added wave resistance, resulting in the required permanent delivered power and the one induced by the waves. The analysis accounts for the ship’s main characteristics, operational profile based on mission conditions, and wave climatic data. All sources of inherent uncertainties are accounted for through the variability in the 3 h extreme value in any sea state in the long term, and the inverse first-order reliability method (IFORM) is employed in predicting the extreme operational carbon intensity indicator (CII). This study develops proper wave scatter diagrams as a function of the route description. The CII measures the energy efficiency of the installed propulsion system, accounting for the ship’s operational characteristics, such as the annual fuel consumption with corresponding CO2 factors, annual distance travelled, and capacity. The present study is limited to one operation route but can be extended to any other possible voyage or sea area. The estimated CII defined from the complete probabilistic characterisation of the sea state conditions conditional to the short-term maximum response is a rational approach that can be used for optimising the ship’s main characteristics, propulsion system, operational profile, and chosen route to achieve the best ship performance and energy efficiency.