Best treatment for baker's cyst on knee?

Identify cause first: A baker's cyst is a cyst on the back the knee, usually filled with fluid from the knee joint itself. The presence of a bakers cyst is typically an indication of pathology in the knee itself. To "treat" a baker's cyst therefore requires that the problem in the knee be treated- the cyst will then typically go away. See an orthopaedic surgeon for further advice.