Based on the existing research work on the modeling and control of cyclically operated high-throughput screening systems, this paper presents the scheduling and control of high-throughput screening systems with uncertainties and disturbances. Different definitions of disturbance decoupling problems are considered in order to achieve the optimal scheduling of high-throughput screening systems. Online scheduling was achieved by computing optimal prefilters and output feedback controllers, which can be computed using residuation theory. The control strategies achieved by the controllers are optimal in the sense of the just-in-time criterion commonly used in industrial schedule practice.