We present an approach for Worst-Case Execution Time (WCET) Analysis of embedded system software, that is generated from Petri net specifications. The presented approach is part of our work towards a Petri net based methodology for the seamless design of embedded real-time systems. One main characteristic of the approach is that standard Petri net analysis methods are utilized during timing analysis in order to improve WCET estimations. Another characteristic is a – compared to existing WCET tools – less hardware dependent result of the timing analysis. This enables us to apply our methods for the design of dynamically changing embedded systems.