It is challenging to treat canine brucellosis due to the immune evading and stealthy characteristic of the causative bacteria, Brucella (B.) canis. Gold nanoparticle aptamer (AuNP-Apt) conjugated antimicrobial peptide (AMP) is a promising alternative to antibiotics for various bacterial infections. However, the toxicity of AuNP-Apt has been variable throughout research, and the in vivo toxic mechanism has not been fully elucidated. This study evaluated the therapeutic potential against B. canis, and the toxicity of AuNP-Apt conjugated antimicrobial peptide, RW-BP100 (AuNP-AptHis-RW-BP100His), in a mouse model. Intravenous (IV) treatment with AuNP-AptHis-RW-BP100His reduced the bacteria burden and histopathologic lesions. The IV treatment also induced CD4+ T cell differentiation and modulated serum cytokine levels. However, high-dose AuNP-Apt was lethal, resulting in tissue accumulation and vessel embolism. Therefore, AuNP-AptHis-RW-BP100His is a promising therapeutic agent for B. canis treatment, but due to its toxicity, further studies are needed for its utilization in clinical practice.