This study zeroes in on a standard double bed ship isolation ward, employing Computational Fluid Dynamics (CFD) to probe airflow arrangements. It scrutinizes three ventilation tactics while altering the contaminant mass flow rate from human exhalation, assessing comfort and cross-infection risks to pinpoint the best ventilation setup. The findings reveal displacement ventilation’s prowess in eliminating contaminants, thwarting cross-infections effectively. The diameter of contaminants exhaled by patients barely affects comfort but impacts indoor contaminant concentrations. This research is pivotal for curbing cross-infections in shipboard wards and offers crucial insights for isolation ward ventilation design on ships during respiratory droplet-borne viral disease outbreaks. It underscores the significance of proper ventilation in mitigating airborne virus transmission, providing a detailed analysis of airflow and contaminant dispersion via CFD. The results suggest displacement ventilation is an apt choice for shipboard isolation wards, offering energy efficiency and low noise. This study aids in devising effective infection control measures in healthcare settings, enhancing safety and comfort in shipboard isolation wards.