Aerococcus urinae, a gram-positive bacterium found in 0.25–4% of urinary samples, is increasingly recognised as a cause of invasive urinary tract infections and bacteraemia. Its true prevalence is likely underestimated due to misidentification as other gram-positive cocci. Advances like matrix-assisted laser desorption ionisation time-of-flight mass spectrometry have improved diagnostic accuracy. Though rare, A. urinae infective endocarditis is being reported more frequently, especially in adults with cardiac and urinary tract abnormalities. Paediatric cases are uncommon but can be severe. We report a case of mitral valve infective endocarditis in a 15-year-old female with congenital heart defects and neurogenic bladder, presenting with embolic stroke. This highlights the need for prompt diagnosis and multidisciplinary management to improve outcomes in this rare but serious condition.