Simultaneous thermal and hydraulic analysis has been completed using SINDA'85/FLUINT for a two-phase ammonia thermal control system proposed for Space Station Freedom Attached Payload Accommodation Equipment (APAE). This analysis provided information on system performance, transient behavior during heat load changes, and control system response. Control system logic and non-equilibrium effects were included in the model. This paper describes the hardware used in this thermal control system and the modelling techniques used to represent it. A brief comparison of the predicted system performance with test results from ground testing of similar systems at NASA Johnson Space Center is also provided.