The use of mathematical modeling and simulation is central to the study of the absorption, distribution, and elimination of therapeutic drugs (pharmacokinetics) and to understanding how drugs produce their effects (pharmacodynamics). From its inception, the field of pharmacokinetics and pharmacodynamics has applied methods of mathematical modeling, estimation, simulation, experiment design, and control in an effort to better understand, quantify, and regulate the processes of uptake, disposition, and action of therapeutic drugs. These methods for pharmacokinetic/pharmacodynamic systems analysis impact all aspects of drug development including in vitro, animal and human testing, as well as drug therapy. Systems analysis methods applied to pharmacokinetic/pharmacodynamic processes confront many challenges related in part to the severe restrictions on the number and type of measurements that are available from laboratory experiments and clinical trials, as well as the variability in the experiments and the uncertainty associated with the processes themselves. Accordingly, specialized pharmacokinetic/pharmacodynamic systems analysis methods have been developed that address these unique challenges. This chapter focuses on the control of pharmacokinetic/pharmacodynamic processes, which has application to the problems of dose regimen design for patient therapy (pharmacotherapeutics) and for the design of clinical drug trials. After a review of the field, a general pharmacokinetic/pharmacodynamic modeling framework is presented and the control problem is presented, followed by a discussion of the enabling computational methods along with an example illustrating the problem and methods.