COVID-19 has emerged as a pervasive global challenge, giving rise to both significant public health concerns and a range of psychological experiences, such as fear, stigma, and post-traumatic stress disorder. Importantly, healthcare professionals have been subjected to immense mental health problems as they battle against this disease. This study aimed to investigate the mediating roles of perceived stigma, self-stigma related to COVID-19, and fear of COVID-19 in the associations between peritraumatic dissociative experiences and post-traumatic stress disorder during a three-wave COVID-19 pandemic (4th [T1], no wave [T2], and 5th [T3]) in Iran. Data were collected from healthcare professionals using the Peritraumatic Dissociative Experiences Questionnaire, Impact of Event Scale-6, Perceived Stigma Scale, Fear of COVID-19 Scale, and Self-Stigma Scale-Short. The results of structural equation modelling demonstrated positive associations between peritraumatic dissociative experiences, perceived stigma, self-stigma related to COVID-19, fear of COVID-19, and post-traumatic stress disorder across all survey waves. Moreover, the study revealed that perceived stigma, self-stigma related to COVID-19, and fear of COVID-19 acted as mediators in the association between peritraumatic dissociative experiences and post-traumatic stress disorder. The implications of these findings highlight the urgent need to address the mental health of healthcare professionals in the aftermath of a pandemic. Policy efforts should be directed towards providing adequate mental health resources and support to mitigate the psychological impact of pandemics on healthcare professionals.