This study proposes an onboard membrane carbon capture and liquefaction system for LNG-fueled ships to satisfy the IMO’s 2050 greenhouse gas reduction targets. The exhaust gas from a natural gas ship has a low CO2 fraction (∼3%) and high O2 fraction (∼16%) compared to the flue gas from power plants. Herein, considering the above distinguishing features, a membrane carbon capture and liquefaction system has been proposed that is energy efficient and compact for the application of ships. To ascertain the performance of the proposed membrane-based system, it is compared to an amine-based onboard system in terms of energy consumption and major equipment size. This work evaluates four process configurations by varying the number of membrane stages and associated liquefaction processes at different CO2/N2 selectivity and CO2 permeance. The results show that energy consumption (3.98 GJe/tLCO2) is higher than the amine-based system (3.07 GJe/tLCO2) at the CO2/N2 selectivity of 50, but it can be decreased to 3.14 and 2.82 (GJe/tLCO2) with an improved selectivity of 100 and 150, respectively. The major equipment size decreases to 54%, 28%, and 20% of the amine-based system when the permeance is 1000, 2000, and 3000 GPU, respectively. The results indicate that the new onboard membrane carbon capture and liquefaction system can be a competitive solution for the IMO’s greenhouse gas reduction targets for 2050.