Background Brucellosis is a zoonotic disease of veterinary, public health, and economic significance in most developing countries, yet there are few studies that show integrated human and veterinary health care intervention focusing on integration at both activity and actors levels. The aim of our study, therefore, was to explore community perceptions on integration of animal vaccination and health education by veterinary and public health workers in the management of brucellosis in Uganda. Methods This study used a qualitative design where six Focus Group Discussions (FGDs) that were homogenous in nature were conducted, two from each sub-county, one with the local leaders, and another with pastoralists and farmers. Five Key Informant Interviews (KIIs) with two public health workers and three veterinary extension workers from three sub-counties in Kiruhura district, Uganda were conducted. All FGDs were conducted in the local language and tape recorded with consent from the participants. KIIs were in English and later transcribed and analyzed using latent content data analysis method. Results All the groups mentioned that they lacked awareness on brucellosis commonly known as Brucella and its vaccination in animals. Respondents perceived improvement in human resources in terms of training and recruiting more health personnel, facilitation of the necessary activities such as sensitization of the communities about brucellosis, and provision of vaccines and diagnostic tests as very important in the integration process in the communities. The FGD participants also believed that community participation was crucial for sustainability and ownership of the integration process. Conclusions The respondents reported limited knowledge of brucellosis and its vaccination in animals. The community members believed that mass animal vaccination in combination with health education about the disease is important and possible if it involves government and all other stakeholders such as wildlife authorities, community members, local to national political leaders, as well as the technical personnel from veterinary, medical and public health sectors since it affects both humans and animals.