As permissioned blockchain becomes a common foundation of blockchain-based applications for current organizations, related stakeholders need a means to assess the security risks of the applications. Therefore, this study proposes a security risk management framework for permissioned blockchain applications. The framework divides itself into different implementation stacks and provides guidelines to control the security risks of permissioned blockchain applications. According to the best of our knowledge, this study is the first research that provides a means to evaluate the security risks of permissioned blockchain applications from a holistic point of view. If users can trust the applications that adopted this framework, this study can hopefully contribute to the adoption of permissioned blockchain technologies.