An 8-year-old castrated male Maltese dog (patient) was referred to our institute with refractory canine babesiosis. The patient had previously responded to conventional treatment with atovaquone and azithromycin; however, anemia had recurred at six weeks after treatment withdrawal. No effect was observed on the administration of the same medication along with diminazene aceturate. On blood analysis, mild anemia was identified, with the absolute reticulocyte count indicating a markedly regenerative state. On Diff-Quik-stained peripheral blood film examination, the parasitic protozoan Babesia gibsoni was observed, and based on further laboratory examinations, a relapse of babesiosis was confirmed. Based on a previous study of drug-resistant variants of B. gibsoni and therapeutic trials, the treatment was then changed to a combination therapy of clindamycin, doxycycline, and metronidazole. Subsequently, the patient’s condition improved rapidly — B. gibsoni was not detected in the blood film and the PCR analysis for it was negative. This treatment was discontinued at six weeks after treatment initiation; however, at seven weeks after the treatment withdrawal, another relapse of babesiosis was confirmed and treatment was restarted with the same protocol. This treatment was effective again and lasted for 12 weeks. However, anemia recurred again at five weeks after withdrawal of the previous treatment and was corrected by restarting the same treatment protocol. This third treatment continued for 24 weeks and was finally stopped at the request of the client. The patient has reportedly been doing well with no manifestation of clinical signs and symptoms. This case report demonstrates that the clindamycin- doxycycline-metronidazole combination therapy against atovaquone and azithromycin-resistant B. gibsoni may be effective in improving the clinical manifestation of symptoms of canine babesiosis and this therapy may be an alternative treatment strategy.