Introduction Unlike previous pandemics, COVID-19 has sustained over a relatively longer period with cyclical infection waves and numerous variants. Public transport ridership has been hit particularly hard. To restore travellers' confidence it is critical to assess their risk determinants and trade-offs. Methods To this end, we survey train travellers in the Netherlands in order to: (i) quantify the impact of trip-specific, policy-based, and pandemic-related attributes on travellers' COVID-19 risk perceptions; and (ii) evaluate the trade-off between this risk perception and other travel attributes. Adopting the hierarchical information integration approach, in a two-stage stated preference experiment, respondents are asked to first rate how risky they perceive different travel situations to be, and then to choose between different travel options that include their own perceived risk rating as an attribute. Perceived risk ratings and choices between travel options are modelled using a linear regression and a mixed multinomial logit model, respectively. Results We find that on-board crowding and infection rates are the most important factors for risk perception. Amongst personal characteristics, the vulnerability of family and friends has the largest impact-nearly twice that of personal health risk. The bridging choice experiment reveals that while values of time have remained similar to pre-pandemic estimates, travellers are significantly more likely to choose routes with less COVID-19 risk (e.g., due to lower crowding). Respondents making longer trips by train value risk four times as much as their shorter trip counterparts. By combining the two models, we also report willingness to pay for mitigating factors: Reduced crowding, mask mandates, and increased sanitization. Conclusion Since we evaluate the impact of a large number of variables on route choice behaviour, we can use the estimated models to predict behaviour under detailed pandemic scenarios. Moreover, in addition to highlighting the importance of COVID-19 risk perceptions in public transport route choices, the results from this study provide valuable information regarding the mitigating impacts of various policies on perceived risk.