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Introduction Occlusion of cerebral arteries account for 40–50% of neurological complications of infective endocarditis with the emboli most commonly lodging in the middle cerebral artery. The management of these occlusions with the use of thrombolytic therapies are associated with intracranial hemorrhage whereas outcomes with endovascular thrombectomy, while still under investigation, appear to be more favorable. In this case report, we present a HIV patient with persistent staphylococcus lugdunenesis bacteremia of unknown origin and acute left middle cerebral artery occlusion, who underwent endovascular thrombectomy. Methods Case Report Results A 66‐year‐old male past medical history of HIV on Elvitegravir/Cobicistat/Emtricitabine/ Tenofovir, pancytopenia and treated hepatitis C who presented for malaise, back pain, and urinary symptoms for 1 week. Initial labs remarkable for pancytopenia, CD4 count 44 and positive urinalysis. Ceftriaxone was started for UTI and Trimethoprim/Sulfamethoxazole for PJP prophylaxis. Urine and multiple blood cultures were positive for staphylococcus lugdunensis. Vancomycin was added to antibiotic therapy. On day two of hospitalization, patient developed new onset aphasia, right facial droop, and right hemiparesis. Upon evaluation, NIHSS was 14. CT head was negative. CTA head and neck showed left M1 occlusion. CT perfusion showed an infarct core of 20cc and 144cc of penumbra. Due to concern for possible infective endocarditis, thrombolytics were not administered but he was taken for thrombectomy. Emboli retrieval was successful with mTICI‐2c reperfusion. During thrombectomy, clot noted to have septic emboli appearance. Post thrombectomy, patient had complete resolution of neurological deficits. MRI brain showed multiple punctate foci of restricted diffusion in the left middle cerebral artery distribution consistent with embolic process. TTE was inconclusive. Intraoperative cultures of the clot resulted positive for staphylococcus lugdunensis and pathology examination detailed clot with bacterial colonization. TEE was performed and negative for valvular vegetations, mass, thrombus, or endocarditis but there was an intrapulmonary shunt. Patient later developed a small acute left parietal lobe parenchymal hematoma and basal ganglia infarct. His neurological status remained unchanged. He completed 6 weeks of IV antibiotic therapy upon discharge. Conclusions This case illustrates the importance of timely endovascular thrombectomy in suspected cerebral septic emboli as outcomes are favorable. It supports prompt recognition of septic emboli bacterial species for targeted antibiotic therapy along with further investigation into staphylococcus lugdunensis and its relation with cerebral septic emboli. This case urges additional exploration into the relationship between HIV patients and cerebrovascular disease including cerebral septic emboli.