The post-effects of COVID-19 have begun to emerge in the long term in society. Stroke has become one of the most common side effects in the post-COVID community. In this study, to examine the relationship between COVID-19 and stroke, a fractional-order mathematical model has been constructed by considering the fear effect of being infected. The model’s positivity and boundedness have been proved, and stability has been examined for disease-free and co-existing equilibrium points to demonstrate the biological meaningfulness of the model. Subsequently, the basic reproduction number (the virus transmission potential (R0)) has been calculated. Next, the sensitivity analysis of the parameters according to R0 has been considered. Moreover, the values of the model parameters have been calculated using the parameter estimation method with real data originating from the United Kingdom. Furthermore, to underscore the benefits of fractional-order differential equations (FODEs), analyses demonstrating their relevance in memory trace and hereditary characteristics have been provided. Finally, numerical simulations have been highlighted to validate our theoretical findings and explore the system’s dynamic behavior. From the findings, we have seen that if the screening rate in the population is increased, more cases can be detected, and stroke development can be prevented. We also have concluded that if the fear in the population is removed, the infection will spread further, and the number of people suffering from a stroke may increase.