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Objective We present a new system to track, manage, and report on all risks and issues encountered during a clinical trial. Materials and Methods Our solution utilizes JIRA, a popular issue and project tracking tool for software development, augmented by third-party and custom-built plugins to provide the additional functionality missing from the core product. Results The new system integrates all issue types under a single tracking tool and offers a range of capabilities, including configurable issue management workflows, seamless integration with other clinical systems, extensive history, reporting, and trending, and an intuitive web interface. Discussion and Conclusion By preserving the linkage between risks, issues, actions, decisions, and outcomes, the system allows study teams to assess the impact and effectiveness of their risk management strategies and present a coherent account of how the trial was conducted. Since the tool was put in production, we have observed an increase in the number of reported issues and a decrease in the median issue resolution time which, along with the positive user feedback, point to marked improvements in quality, transparency, productivity, and teamwork.