BackgroundPublic transportation plays a major role in the transmission of SARS-CoV2, the virus that causes COVID-19, due to the confined spaces in vehicles. It is therefore very crucial to apply COVID-19 prevention measures in public transportation to reduce risk of COVID-19 transmission. The implementation of these measures depends largely on the public transportation users. We explored the awareness, perceptions and challenges among public transport operators during the implementation of COVID-19 preventive measures in Eastern Uganda.MethodsThis qualitative study was done in Eastern Uganda in January and February 2021. We conducted four focus group discussions, six in-depth interviews and three key informant interviews to document the awareness, perceptions and challenges faced by public transport operators including 10 boda boda riders, 19 taxi operators and 11 truck (cargo) transporters. All interviews were audio-recorded, transcribed verbatim, and analyzed with the help of NVIVO software version 12 plus using a thematic framework approach.ResultsWe relied on the health belief model to report on four broad themes including: Perceived threat, perceived benefits, perceived barriers and cues to action.Perceived threatParticipants were aware of the gravity / seriousness of COVID-19. They were aware that it is an unusual flu whose symptoms are severe and clearly distinguishable from the common flu. They also knew that COVID-19 is easily and quickly transmitted. However they were not aware of the cause of COVID-19. Perceived benefits: the participants perceived a number covid 19 preventive measures as beneficial in preventing COVID-19. These included: COVID 19 vaccination, observing hand hygiene, avoiding touching the ‘soft parts’ (eyes, nose and mouth), quarantining in a hospital setting, wearing a face mask, social distancing,. Perceived barriers: participants reported barriers to implementing COVID 19 preventive measures included Misconceptions about COVID 19, scepticism about COVID-19 vaccination, not breathing well or respiratory problems hinders use of face masks, fear of covid 19 transmission during home isolation, design of the vehicles do not favour social distancing, passengers unwilling to pay the fare, natural reflexes come in the way of not touching soft parts, financial constraints, hostility from passengers due to increased transport fares, law enforcement officials prioritizing the driving permit over implementation of the measures, hostility from law enforcement officials, religious beliefs against the use of alcohol, competing for passengers among public transporters.Cues to action includedMass sensitization by the Ugandan government through the ministry of health with the help of media platforms like television.Conclusions and recommendationOur study brings to light the likely barriers that impede the use of preventive measures in public transportation use during an epidemic / pandemic like COVID-19 which could potentially escalate transmission. During cues to action like sensitization through media, focus should be put to the demystification of myths on COVID-19, highlighting on benefits of using preventive measures and risk of disease. Public transport passengers should be sensitized on risk of COVID-19 transmission during public transportation use and on the importance of complying with COVID-19 preventive measures. We recommend further exploration on the challenges faced by the public transportation passengers in implementing preventive measures in the event of an epidemic like COVID-19. Future research is required to establish a more robust transport model in crisis situations such as a pandemic. In addition, there is need for integration between the public health and public transportation sectors to foster epidemic preparedness for future crises in the context of public transportation.