This research creates an operations engineering and management methodology to optimize a complex operational planning and coordination challenge faced by sites that perform clinical research trials. The time-sensitive and resource-specific treatment sequences for each of the many trial protocols conducted at a site make it very difficult to capture the dynamics of this unusually complex system. Existing approaches for site planning and participant scheduling exhibit both excessively long and highly variable Time to First Available Visit (TFAV) waiting times and high staff overtime costs. We have created a new method, termed CApacity Planning Tool And INformatics (CAPTAIN) that provides decision support to identify the most valuable set of research trials to conduct within available resources and a plan for how to book their participants. Constraints include (i) the staff overtime costs, and/or (ii) the TFAV by trial. To estimate the site’s metrics via a Mixed-Integer Program, CAPTAIN combines a participant trajectory forecasting with an efficient visit booking reservation plan to allocate the date for the first visit of every participant’s treatment sequence. It also plans a daily nursing staff schedule that is optimized together with the booking reservation plan to optimize each nurse’s shift assignments in consideration of participants’ requirements/needs.