Background: Ebola Virus Disease (EVD) presents with a high global mortality and is known to be a highly infectious disease with devastating and gendered effects on the social fabric, yet most of the science has focused on the disease’s biology. However, little has been documented with regard to the gender and social aspects of Ebola Virus Disease (EVD) in two sub counties (Kikyo and Bundibugyo Town Council) in Bundibugyo District in Western Uganda. The study was set to examine the gender differences in the level of knowledge, attitudes and perceptions about EVD. Methods: The study employed a cross-sectional design using both quantitative and qualitative data collection methods. A structured questionnaire was administered to 254 respondents, 50% of whom were women. Simple random sampling was used to select the participants. Questionnaire data were analysed using SPSS at univariate and bivariate levels. Qualitative methods such as key informant interviews (with 6 participants) and Focus Group Discussions (three, one with men alone, another with women alone and the last one with both men and women) were also used to collect additional information from participants. Results: The findings indicated that socio-demographically, the majority (35%) of the respondents were aged between 20 and 29 years, 53% of whom were females. More women (about 56%) compared to men (44%) attained secondary education while more men (about 51% versus 49% of the women) reported that they were married. In terms of religion, the majority of the survey participants were Catholics (59% females and 49% males). With regard to communities’ knowledge about EVD, there was no significant relationship between men and women in terms of prior knowledge about EVD, risk factors and control measures. However, slightly more males (about 51%) than females (49%) had heard about EVD and more males (about 52%) than females (48%) admitted that they were at risk of contracting the disease. On the control measures, slightly more females than males (about 53% vs