Previously, the Petri nets were used as modeling tools not a designing tool for discrete event controllers (DEC's). In addition, there is a lacking to extract the mathematical model of the controller based on the Petri net. In this paper, a Dynamic Petri Net (DPN) is proposed to design a controller for the discrete event systems (DES's). The design procedure of the DPN based DEC is introduced. The proposed procedure has been investigated through designing controllers for many case studies, which represent real industrial discrete event flexible manufacturing systems. One of these controllers has been extensively tested experimentally. Both the theoretical and experimental results of the performance of this controller are introduced. Comparing and analyzing these results have been confirmed the validity of the proposed DPN based DEC and showed that the proposed technique offers many advantages such as its mathematical model base beside the graphical representation of the whole DES.