The Polymer Electrolyte Membrane Fuel Cell is a widely researched fuel cell, and a highly potential candidate for alternate power generation. However, technical issues such as membrane flooding and drying prevent its deployment in many applications. Electrochemical Impedance Spectroscopy (EIS) is a very powerful technique that is used to isolate flooding and drying of the fuel cell from operating data. Such information about the state of operation of the cell is critical to deciding necessary control actions to maintain the health and performance of the cell. However, the time taken in obtaining measurements in EIS can be large enough to allow the cell to flood or dry beyond irreparable damage, rendering it a mere postmortem technique. Moreover, after long durations of perturbation, the cell takes a considerable amount of time to return to its regular operation. A new technique is proposed that uses the concept of EIS, but is computationally faster and gives results comparable with those of traditional EIS. This technique is based on perturbing the cell with a small chirp signal containing large number of frequencies instead of series of small sinusoids at different frequencies. Simulation results on isolation of flooding and drying based on Fast EIS are illustrated and future work directions are indicated. © 2015 American Automatic Control Council.