This report describes a pregnant lady in early trimester that was admitted with fever and left loin pain and was initially treated as presumed pyelonephritis. Subsequently she was found to have infective endocarditis with vegetation on the mitral valve. The course of her illness was complicated by acute pulmonary edema and septic embolization to the cerebellum. A decompressive craniectomy and resection of the lateral lobe of cerebellum was performed. Although the presenting features and risk factors are well described, the atypical presentations of infective endocarditis in pregnancy remain a diagnostic challenge for the treating physician. This report highlights the importance of rapid detection of endocarditis in pregnancy and the treatment of systemic complications.