A 55-year-old women was diagnosed with Baker's cyst and underwent open Baker's cyst excision. She had developed acute pulmonary embolism in the post-operative period. Our case report is to emphasise the sub-clinical concomitant deep vein thrombosis with Baker's cyst. Such a fatal complication has not been reported in literature and preventive measures of pre-operative venous Doppler and post-operative thrombo-prophylaxis can prevent them.