BACKGROUND Aerococcus species are a rare cause of endocarditis. Micro-organism identification and antibiotic choice can pose significant management challenges to clinicians who care for patients with this infection. Aerococcus is a gram-positive micro-organism which is commonly misidentified because it shares many similarities with streptococcus and enterococcus species. Aerococcus urinae is usually found to cause urinary tract infections and occurs more frequently in patients with structural urinary tract abnormalities associated with urethral and ureteral obstruction such as kidney stones, phimosis, and prostate hyperplasia. However, it is reported to rarely cause endocarditis. CASE REPORT A 48-year-old man with a history of cocaine abuse and right hip replacement presented to our emergency department with acute encephalopathy. Through a complicated hospital course, he was found to be septic and the bacteria were initially misidentified as an alpha-hemolytic strep before being correctly identified as Aerococcus urinae. He was found to have multiple cerebral, likely septic, embolic infarcts and aortic valve endocarditis. Identification of the micro-organism on blood cultures was challenging, as were decisions about antibiotic choice. He died despite efforts of a multidisciplinary care team. CONCLUSIONS Our case highlights a unique case of Aerococcus endocarditis and shows the difficulty in initially identifying the bacteria. To our knowledge this is the first case reported in the setting of substance abuse. It also highlights the lack of appropriate guideline-directed therapy with regards to antibiotic choices in this group of patients, emphasizing the importance of further research in this regard.