We present the case of a 35-year-old female with small restrictive ventricular septal defect (VSD) presenting with prolonged fever for the last 1 month with vegetation on the right coronary cusp (RCC) of the aortic valve with flail aortic leaflet causing severe aortic regurgitation (AR). Her echocardiography done 1 year back had revealed the presence of small restrictive VSD with a gradient of 80 mm Hg without any prolapse of RCC or presence of AR. She did not have any early diastolic murmur of AR during 3 monthly routine follow-up in the cardiology outpatient department suggestive of previous aortic valve prolapse with AR in the aforesaid period before the infective endocarditis episode. Common sites of the vegetation in small restrictive VSD are right ventricular side of the interventricular septum, undersurface of the tricuspid valve, free wall of the right ventricle, and rarely the pulmonary valve on the low-pressure site of the shunt where the turbulent jet containing the bacteria slows down, and bacteria adhere the underlying endocardium. Normally, vegetation across any turbulent jet does not occur on the high-pressure site due to the reason that bacteria can not adhere to the wall across the turbulent jet in high-pressure zone, which sweeps away all the bacteria from the high-pressure zone to low-pressure zone. Paradoxical finding in our case was that vegetation was noted on the RCC of the aortic valve which was a high-pressure zone, which may be explained by only Bernoulli's phenomenon. Our case illustrates paradoxical vegetation on the RCC of the aortic leaflet in a patient with small restrictive VSD and is also a unique demonstration of left-sided endocarditis in a patient with left-to-right shunt.