System thermal-hydraulics codes evaluate the thermal-hydraulics of the entire primary circuit (unlike core thermal-hydraulics codes, which only evaluate the thermal-hydraulics in the core). The thermal-hydraulics of the secondary circuit may also be evaluated, since this can affect the coolant enthalpy. The core is generally modelled as in core thermal-hydraulics codes, but with a lesser degree of discretisation. The remainder of the primary circuit (and possibly also the secondary circuit) are divided into various components, which are connected by sections of pipework.

The fluid mass, momentum and energy conservation equations are solved for each component and pipework section using similar techniques to those described for core thermal-hydraulics codes, but with sub-models for specific components such as coolant pumps, valves, etc., which allow their effects on the working fluid to be calculated without explicit modelling of the components themselves. In order to simulate the effects of automated, or reactor operator initiated, control of components, a control system model is also required. (This can, for example, simulate automated opening of pressure relief valves when the fluid pressure exceeds a trip setpoint.) Finally, a transient neutronics module is often integrated into the code to model the coupling between the core neutronics and the core thermal-hydraulics during certain events (e. g. a steamline break in a PWR or power-flow oscillations in a BWR); alternatively, the system thermal-hydraulics code can be coupled to a whole core neutronics code.

Both steady-state and transient simulations are generally possible with system thermal-hydraulics codes. A typical application is the determination of the evolution of the fluid boundary conditions in the core for a specific fault, such as a loss of coolant accident (LOCA) in an LWR. The results can then be fed to a core thermal-hydraulics code for more detailed analysis of the thermal-hydraulics in the core, or directly to a transient fuel performance code for thermo-mechanical analysis of the fuel pins.