Alternative control schemes for an Advanced High Temperature Reactor system consisting of a reactor, an intermediate heat exchanger, and a secondary heat exchanger (SHX) are presented in this paper. One scheme is designed to control the cold outlet temperature of the SHX (Tco) and the hot outlet temperature of the intermediate heat exchanger (Tho2) by manipulating the hot-side flow rates of the heat exchangers (Fh/Fh2) responding to the flow rate and temperature disturbances. The flow rate disturbances typically require a larger manipulation of the flow rates than temperature disturbances. An alternate strategy examines the control of the cold outlet temperature of the SHX (Tco) only, since this temperature provides the driving force for energy production in the power conversion unit or the process application. The control can be achieved by three options: (1) flow rate manipulation; (2) reactor power manipulation; or (3) a combination of the two. The first option has a quicker response but requires a large flow rate change. The second option is the slowest but does not involve any change in the flow rates of streams. The third option appears preferable as it has an intermediate response time and requires only a minimal flow rate change.