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Most clinics rely on the appointment scheduling systems to manage patients' access to their health-care providers. Conventional appointment scheduling processes have intrinsic inefficiency because of the tendency to generate fragmented time slots. In this article, a solution, which considers patient-provider mutual preference, is provided to guide the appointment scheduling process by means of schedule defragmentation. Computer simulation shows that patient-provider cooperation can effectively reduce schedule fragmentation, yielding higher appointment acceptance rate and clinic time utilization rate at given appointment demand matched by service supply. When service time distribution can be accurately estimated, decreasing unit time slot size may further improve the appointment scheduling efficiency. In addition, a clinical survey was conducted to identify the opportunities and challenges of applying the proposed defragmentation method in clinical appointment scheduling practice.