A 23-year old male of South-Asian ethnicity, presented with fever and cough of one month duration. Examination revealed pansystolic murmur in tricuspid area, ejection systolic murmur in pulmonary area and a normal second heart sound. Echocardiogram showed tricuspid valve vegetations with mild to moderate Pulmonary artery hypertension (PAH) with non dilated right atrium and right ventricle. Blood Cultures for typical and atypical organisms of endocarditis were sterile. Anti-nuclear antibody (ANA) turned out to be positive but ds-DNA and anti-sm were negative. Lupus anticoagulant and anti cardiolipin antibody were positive in high titers. CECT thorax revealed thrombotic occlusion of left main pulmonary artery (LMPA). Criteria for Systemic lupus erythematosus (SLE), was not met initially, developed subsequently during the course of the disease. He was finally diagnosed as Anti-Phospholipid Antibody Syndrome (APS) secondary to SLE. This is a rare case of APS presenting as right sided endocarditis in a young male. Initially confused for Infective Endocarditis but finally diagnosed as APS secondary to SLE.