Intelligent work zone (IWZ) systems use innovative technologies in real time to mitigate the negative impacts of work zones on the traveling public. The automatic queue detection (AQD) system is one type of IWZ being promoted by the Federal Highway Administration. Several field studies found that AQD systems were successful in reducing average travel speeds which led to a reduction in the number of rear-end crashes and in user costs. It has been shown that well-calibrated microsimulation models are appropriate analysis tools for traditional work zone traffic. To date, there are no tools in the literature that have been developed for AQD operations that have been calibrated and validated with empirical data. This paper aims to fill this gap by providing a comprehensive guideline for calibrating and validating a microsimulation model that can emulate traffic conditions and their impacts on freeway IWZ equipped with AQD systems. Specifically, the methodology includes (1) developing the base work zone model, (2) replicating the AQD warning messages, (3) calibrating the key simulation parameters using three types of data, and (4) validating the resulting simulation model using segment travel times. This comprehensive approach was demonstrated on a Nebraska work zone that was equipped with an AQD system. VISSIM simulation model was used for the underlying tool in the demonstration. The results presented in this paper are useful to both practitioners and scholars who wish to study the impact of the IWZ accurately through microsimulation.