After a fatal accident during the discharge of wood pellets at Helsingborg, emissions from pellets during marine transportation became a concern for the safe handling and storage of wood pellets. In this paper, a two-compartment model has been developed for the first time to predict the concentrations of CO, CO2, CH4, and O2 inside the cargo ship and the time and rate of forced ventilation required before the safe entry into the stairway adjacent to the storage hatch. The hatch and stairway are treated as two perfectly mixed tanks. The gas exchange rate between these two rooms and the gas exchange rate with the atmosphere are fitted to satisfy a measured tracer final concentration of 33 p.p.m.v. in the stairway and an average final hatch to stairway CO, CO2, and CH4 concentration ratio of 1.62 based on measurement from five other hatch and stairway systems. The reaction kinetics obtained from a laboratory unit using a different batch of pellets, however, need to be scaled in order to bring the prediction to close agreement with onboard measured emission data at the end of voyage. Using the adjusted kinetic data, the model was able to predict the general trend of data recorded in the first 12.5 days of the voyage. Further validation, however, requires the data recorded over the whole journey. The model was applied to predict the effect of ocean temperature on the off-gas emissions and the buildup of concentrations in the hatch and stairway. For safe entry to the cargo ship, the current model predicted that a minimal ventilation rate of 4.4 hr−1 is required for the stairway's CO concentration to lower to a safe concentration of 25 p.p.m.v. At 4.4 hr−1, 10 min of ventilation time is required for the safe entry into the stairway studied.