1 Overall, the complete treatment session can range anywhere from $29,000 to as much as $62,000 without any sort of insurance policy. 2  Medicare currently pays around $19,000 for a full dosage. 3  NPR says that you should budget at least $50,000 per patient. Medicare currently pays around $19,000 for a full dosage. 2  NPR says that you should budget at least $50,000 per patient. 3  According to other sources such as wikipedia.org, proton therapy is very expensive compared to other forms of cancer treatment. 4  A proton facility costs as much as $200 million to construct.