The purpose of this article is to examine the cause of policy non-compliance in the case of pharmaceutical rebates from the perspective of rational choice institutionalism. In Korea, there have been rebates practices between pharmaceutical companies and hospitals since the introduction of the Actual Remuneration System for insured medicine in 1999. The government has chosen the policy means of punishment to eliminate pharmaceutical rebates but the illegal practices are still widespread. Institution in rational choice institutionalism usually reflects the incentives and preferences of actors, and the Actual Remuneration System has resulted in a the lack of procedures to ensure savings on drug expenditures. Pharmaceutical rebates are the product of the institutions which reflect their incentives: the Actual Remuneration System, the current pricing policy for generic drugs, the drug distribution system, and so on. In the end, the problem of the rebates is the consequence of policy non-compliance as actors' rational choice because their incentives lead to opportunistic behaviors. We should therefore understand the incentive structure of policy stakeholders, which is derived from the view of new institutionalism; also, the newly designed Korean drug pricing policy reform must be compatible with the incentive structure.