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Though you may be able to treat your Baker's cyst at home, you want to make sure it is, in fact, a Baker's cyst and not something that requires medical attention, such as deep vein thrombosis or arterial obstruction. If you experience swelling or  purplish marks in the toes and feet, you should see a doctor right away. You should rest your knee until it no longer hurts to put pressure on it. Note any pain you specifically feel around or behind your knee while flexing and extending your leg. You should rest your knee as often as possible for at least a day or two. You should ice your knee injury as soon as possible. Icing helps reduce swelling and inflammation around the injury, which will also help relieve some of the pain. Only leave the ice on your knee for fifteen to twenty minutes at a time. Allow the area to warm to room temperature (another fifteen to twenty minutes) before reapplying the ice. This can help reduce swelling and pain for the first day or two after the initial injury, and you can ice your knee as often as you want during this period. Wrap a bag of ice (or something frozen, like a bag of peas) with a towel (never directly to the skin) before you apply it. A compress helps reduce swelling to the injured area, and it also helps to stabilize your knee. Tie an elastic bandage (ace wrap), trainer's tape, a brace, or even a piece of clothing around the injury. Tie it tightly enough to stabilize your knee but not so tightly that you cut off circulation. Elevating your leg also helps reduce swelling, and it returns blood to the heart. While laying down, raise your leg above the level of your heart (or as high as you can without causing pain). If you can't raise the injured leg, try to keep it at least parallel to the ground. Also try placing pillows under your legs when sleeping to keep them elevated. You can take non-steroidal anti-inflammatory drugs (NSAIDs) such as ibuprofen, acetaminophen, aspirin, and naproxen, to help reduce pain and swelling. Follow the dosage on the label and stay within the recommended daily allowance. Take medications with meals and water.  Aspirin should not be given to children or adolescents under 19 due to the possibility of Reye syndrome (brain and liver damage), especially if the child has chickenpox or the flu. Talk to your doctor before giving aspirin to your child. Medical professionals recommend consulting your doctor before taking NSAIDs if you have liver, kidney, or stomach issues.

Summary:
Know the difference between a Baker's cyst and something more serious. Rest your affected knee. Ice your knee around the cyst. Use a compress. Elevate your leg. Take an over-the-counter (OTC) pain medication.