A system and method are provided for maintaining alignment of timing signals of a source synchronous interface between driver and receiver portions of an electronic system in a behavioral model based simulation environment. The system comprises a memory unit, an analysis controller unit coupled to the memory unit, and a timing alignment unit coupled to the analysis controller unit. The timing alignment unit is executable responsive to the analysis controller unit to generate behavioral models for mutually assigned first and second nets which transmit respective timing signals between the driver and receiver portions, and actuates transient simulation on the behavioral models to simulate transmission of the timing signals through the first and second nets. A timing skew between respective transmissions of the timing signals through the first and second nets is measured responsive to the simulated transmission for compensation during a general simulation of the source synchronous interface.