Cardiac disease in young children can be unrecognized until symptoms are unmasked by a precipitating event, such as an infection. We present a case of anomalous left coronary artery from the pulmonary artery causing clinically significant disease in a four-month-old male with concomitant mitral regurgitation and pulmonary coccidioidomycosis who required modification of his surgical management due to the infection. This case highlights how timely diagnosis and perioperative management and recovery can be affected by concurrent infections in patients with congenital heart disease.