In this article, we seek to formulate a robust mathematical model to study the Ebola disease through fractal-fractional operators. The study thus incorporates the transmission rate in the treatment centers and the relapse rate, since the Ebola virus persists or mostly hides in the immunologically protected sites of survivors. The Ebola virus disease (EVD) is one of the infectious diseases that has recorded a high death rate in countries where it is endemic, and Uganda is not an exception. The world at large has suffered from this deadly disease since 1976 when it was declared epidemic by the World Health Organization. The study employed fractal-fractional operators to identify the epidemiological patterns of EVD, especially in treatment centers and relapse. Memory loss and relapse are mostly observed in EVD survivors and this justifies the use of fractional operators to capture the true dynamics of the disease. Through dynamical analysis, the model is proven to be positive and bounded in the region. The model is further explicitly shown to have a solution that is unique and stable. The reproduction number was duly computed by using the next-generation matrix approach. By taking EVD epidemic cases in Uganda, the study fitted all parameters to real data. It has been shown through sensitivity index analysis that the transmission rate outside treatment centers and relapse have a significant effect on the endemic state of the disease, as they lead to an increase in the basic reproduction ratio.