Background: Baker’s cyst is synovial swelling, found in the popliteal fossa seen typically in adults. In children, it is relatively rare, which at times may require surgical excision, which has its own morbidity. We evaluated the results of threading technique in children having Baker’s cyst. Methods: 6 cases of age less than 15 years with baker’s cyst who failed to respond to conservative treatment were treated by our threading and aspiration technique. Ultrasound was used to confirm the diagnosis. Results: 6 male children with mean age of 10 years with failed conservative treatment for mean of 5.5 months were included in study. Mean aspirate of cyst was 12.5 ml and mean time of thread removal was 7.1 day. Swelling of Baker’s cyst subsided in all cases in mean time to 6.4 weeks (range 6 to 8 weeks) completely without any recurrence at final follow of 1 year. Conclusion: Threading technique is good alternative to surgical excision in treatment of baker’s cyst in children, with advantages of easy, cost effective, low morbidity, day care procedure without loss to school days