The planar design of printed circuit board (PCB) fuel cells offers the advantages of simple structure, rapid prototyping and easy manufacturing. However, uneven reactants and heat distribution in each PCB cell module often result in inconsistent overall performance. Current characterisation methods mainly focus on the study of the overall performance and lack the analysis of individual cells, which provide a limited understanding of localised electrochemical and thermal effects that might play a critical part in further optimising and diagnosing the cell performance of this category. We have developed a multi-channel impedance diagnostic technique for PCB fuel cells. Combining with thermal imaging, we could simultaneously diagnose individual open cathode cell modules by measuring the heat distribution and electrochemical impedance spectra (EIS) of 11 PCB cell modules. Hence, the correlation between heat distribution, internal resistance and performance of different sections of PCB fuel cells can be established. By comparing the fuel cell’s pristine and degraded, we demonstrated how this non-destructive technique could identify and locate cell modules with deteriorated performance, which would be beneficial to real-time diagnostics, quality control and optimisation. The multi-channel impedance measurement takes several seconds only through optimised multi-frequency perturbation and can be readily extended to stacks containing more cells by simply increasing the number of voltage sensors, which can be further adapted to other electrochemical devices.