Rail transit systems around the world have been suffering from heavily reduced ridership due to reduced capacity for social distancing and passengers’ concern over the risk of COVID-19 infection. Various countermeasures were implemented to reduce the COVID-19 risk so that passengers felt safe to travel on rail. The objectives of this study were to evaluate COVID-19 countermeasures of Bangkok’s urban rail from passengers’ viewpoints and examine its influence on passenger’s confidence. The background of the COVID-19 pandemic in Thailand and the rail countermeasures implemented in Bangkok were summarized. The data were obtained from an interview survey of 1105 railway passengers conducted at the stations during the second wave of the pandemic. Factor analyses and structural equation modeling were conducted. The results revealed that social distancing was not satisfied by the passengers but adversely caused inconvenience and increased infection risk when the station or rail were congested. On the other hand, the passenger temperature check, face mask enforcement, and hand sanitization countermeasures were found to highly and positively contribute to passengers’ confidence. Contact tracing application was also found to raise awareness and confidence. The findings provided insights for rail authorities and related agencies to effectively implement the countermeasures that would be practically and financially sustainable.