Background Highly pathogenic avian influenza (HPAI) H5N1 viruses of clade 2.3.4.4b have recently caused widespread outbreaks in mammals, including domestic cats that live closely with humans and other animals. In-depth molecular and pathological characterizations of naturally infected cats are urgently needed for developing better strategies to prevent interspecies transmission and further spreading of these viruses. Case Summary In this case report, we characterized a unique case of HPAI H5N1 virus infection in an immunocompromised domestic cat. The pet animal was a diabetic cat with a history of feline infectious peritonitis (FIP). In early 2025, the cat developed acute fever and rapidly worsening respiratory distress and liver dysfunction despite antibiotic treatment. Due to severe clinical deterioration, the cat was euthanized. Postmortem examination revealed severe bronchointerstitial pneumonia, hepatic and lymphoid necrosis, bone marrow degeneration, and mild lymphohistiocytic meningitis. H5N1 viral RNA/antigens were specifically detected in the lung, brain, urine, or lymphoid tissues. Whole-genome sequencing and phylogeny analysis identified that the virus belongs to influenza clade 2.3.4.4b (B3.13 subgroup), closely related to HPAI H5N1 strains that are currently circulating in domestic cats and cattle. The source of infection for this particular cat might be linked to a fomite/environmental transmission route. Conclusion The lethal HPAI H5N1 virus infection in an immunocompromised cat highlights the need for developing an improved prevention plan for pet animals. Clinicians should consider the possibility of H5N1 virus infection in cats with similar acute respiratory or neurologic signs, particularly in animals with chronic illness.