The Burkholderia cepacia complex (Bcc) is a group of bacteria with similar biological properties which are an important cause of opportunistic infections. Identification of the Bcc species is important to understand clinical outcomes in human patients. However, there are few studies of Bcc species infecting companion animals such as cats. This report shows for the first time an infection with B. pseudomultivorans, a member of Bcc, in veterinary medicine. A 9-year-old, FIV-positive, mixed-breed cat was subjected to immunosuppressive therapy, developed septic shock, and died. In the bone marrow specimen collected postmortem, numerous short bacilli—some of which were phagocytosed by leukocytes—were observed. By bacteriological examination, the Bcc-like bacteria were isolated from the bone marrow sample. Genetic analysis showed that the recA gene sequence detected from the present case exhibited the highest homology (98–100%) to that of B. pseudomultivorans. Based on these examinations, the present case was diagnosed as B. pseudomultivorans infection. The findings of this study highlight the need for investigation of the Bcc species in veterinary practice to help in treatment decisions and the prognostic evaluation of Bcc infections.