The changing operational requirements and demands for new capabilities, often makes it necessary for systems architects to make substantial changes in a system's architecture. However, the traditional systems engineering processes advocate finalization of architecture at early stages of the design process with little or no change at the later stages of the design. The simulation development is often done towards the end of the design phase and thus, the traditional systems engineering approaches do not support a rapid architecture evolution. In this paper, we propose a Model‐Based Systems Engineering (MBSE) process to facilitate rapid evaluation of changes in a system architecture and/or design artifact for complex systems. This process specifies the minimum set of information that needs to be included in system architecture using SysML diagrams with traceability between the diagrams and agent‐based simulation (ABS) models of a complex system. We demonstrate this SysML‐driven analysis approach to perform a rapid evaluation of evolving system architectures using a NASA‐sponsored project to analyze ab initio architectures for the National Airspace System. We also demonstrate how the proposed approach enables early‐on investigation during the architecture development whether an architecture will yield the desired operational benefit.