A system and method for providing cost-benefit analysis for treatment of a chronic disease such as cancer. The system enables a user to provide input parameters related to a patient, and performs statistical and computational analysis of case histories of other patients and retrospective data related to one or more disease treatment protocols to generate a set of output parameters (potential outcome of the treatment protocols) along with their statistical significance and probability. In addition, the system estimates the cost associated with the treatment protocols using cost related information available for tests, procedures, surgeries, etc., to be performed in a treatment protocol. The average cost and the set of output parameters are displayed to the user which helps in performing the cost-benefit analysis.