We report on the effects of surface roughness resulting from an ion milling technique on the hydrogen gas sensing performance of a single Pd nanowire grown by electrodeposition into nanochannels in anodized aluminum oxide templates. A combination of electron beam lithography and a lift-off process was utilized to fabricate four-terminal devices based on individual Pd nanowires. These results are the first demonstration of the effect of ion milling on the response time in a single Pd nanowire used as a hydrogen sensor. The response time of the single Pd nanowire surface-treated by ion milling was 20 times faster than that of a sample without surface treatment. The faster response time was due to the surface roughness effects of the surface treatment, an increase in the surface-to-volume ratio of the ion-milled nanowire.