A dynamic model of a Direct Methanol Fuel Cell is developed in the MATLAB platform. A newly proposed Coefficient Diagram based Proportional Integral Controller (CD-PIC) is designed and its parameters are calculated. The newly designed CD-PIC is implemented in a real time Direct Methanol Fuel Cell (DMFC) experimental setup. Performances in real time operation of the Direct Methanol Fuel Cell (DMFC) are evaluated. The performance of CD-PIC is obtained under tracking of set point changes. In order to evaluate the CD-PIC performances, most popular tuning rules based Conventional PI Controllers (C-PIC) are also designed and analyzed. Set point tracking is carried out for the step changes of ±10% and ±15% at two different operational points. The controller performances are analyzed in terms of Controller Performance Measuring (CPM) indices. The said performance measures indicate that the proposed CD-PIC gives the superior performances for set point changes and found very much robust in controlling DMFC.