This study examines the impact of COVID-19 on intercity travel mode choices in Mazandaran province, Iran, addressing critical gaps in understanding how pandemics affect travel behavior in developing countries. The research focuses on how socio-economic factors, perceived health risks, and travel time influence individuals’ choice of transportation modes during the pandemic. Using a stated preference survey method with 669 participants, the study assessed how concerns about virus transmission and adherence to health protocols shape travel decisions. Discrete choice modeling was employed to predict travel mode shares between public transport and personal vehicles. The findings reveal that COVID-19 risk perception, socio-economic factors, and travel time significantly impact travel behavior. Specifically, heightened perceived risk of infection resulted in a 25% reduction in public transportation use, with individuals increasingly opting for personal vehicles. Additionally, strict adherence to health protocols, such as mask-wearing and vehicle cleaning, improved safety perception, leading to a 40% increase in confidence in public transport. The study also found that socio-economic factors like age, income, and education significantly shaped travel preferences. These insights provide valuable guidance for public health policymakers and transportation authorities to enhance the safety and management of intercity travel during ongoing and future pandemics.