The aircraft environmental control system (ECS) is a highly integrated and complex system. The passenger air conditioner (PACK) is the heart of the ECS and has been reported as a key driver of unscheduled maintenance by aircraft operators. This is principally due to the PACK’s ability to compensate for degraded components, and hence mask their real condition, so that when failure occurs it is a major event. The development of an accurate diagnostic solution would identify the degradation early and hence focus effective maintenance and reduce cost. This paper is a continuation of the authors’ work on the development of a systematically derived PACK simulation for accurate fault diagnostics, utilizing a model-based approach. In practice, the PACK simulation accuracy is dependent on a number of factors, which include the understanding of its control system. The paper addresses this by taking an in-depth look at the factors controlling the operation of the PACK to enable the gap between the theoretical understanding of the PACK and the engineering design of the system to be bridged, and accurate simulations under healthy and degraded scenarios obtained. This paper provides a comprehensive explanation of the PACK control system elements (principally valves) and verifies their operation based on experimental test data acquired from a B737-400 aircraft. A discussion of the control used in the simulation is then given, resulting in the correct temperature, pressure, and flow being delivered to the cabin. The overall simulation results are then presented to demonstrate the importance of using a systematically derived control logic. They are then further used to assess the impact of degradation in the main PACK valves (PVs).