OBJECTIVE To optimize the free examination, traceability, cost settlement and privacy protection during the development of pediatric drug clinical trials by means of information technology, so as to improve the efficiency and quality of project operation. METHODS Based on the existing hospital information system, multi department joint designed and implemented an information system for the settlement of the diagnosis and treatment expenses for drug clinical trial, which realized the real-time settlement of medical costs for drug clinical trials without the need for advance reimbursement of subjects' guardians. RESULTS This system took into account both cost and function, and had good feasibility. It could effectively improve the operation efficiency of drug clinical institutions, ensure the traceability of diagnosis and treatment data, and optimize the experience and privacy protection of child subjects. CONCLUSION The development and design of this system can effectively improve the operating efficiency of pediatric drug clinical trials, and has a good reference for other new record institutions to solve such problems.