A surface discharge device composed of microns‐thick hollow quartz fibers is used to inactivate resistant fungi cells. The homogeneous cold plasmas are generated by using a pulse high‐voltage source with the repetition frequency of 150 Hz at atmospheric‐pressure. Increasing pulse voltage slightly from 26 to 34 kV leads to an obvious improvement in the inactivation efficiency of fungi cells. The atmospheric‐pressure air plasma generated at the pulse voltage of 34 kV is found to kill the fungi cells as much as 99% within a treatment time of 5 min. The inactivation efficiency is systematically investigated as a function of the processing depth of surface plasma. Various measurements indicate that plasma activated derivatives, such as OH, O, O3, and charged species play a key role in this plasma inactivation process.