The present study aimed to investigate whether gap-prepulse inhibition (GPI) deficit in patients with tinnitus occurred in the N1-P2 complex of the cortical auditory evoked potential. Auditory late responses to the intense sound of the GPI paradigm were obtained from 16 patients with tinnitus and 18 age- and hearing loss-matched controls without tinnitus. The inhibition degrees of the N1-P2 complex were assessed at 100-, 50-, and 20-ms gap durations with tinnitus-pitch-matched and non-matched frequency background noises. At the 20-ms gap condition with the tinnitus-pitch-matched frequency background noise, only the tinnitus group showed an inhibition deficit of the N1-P2 complex. The inhibition deficits were absent in both groups with longer gap durations. These findings suggested that the effect of tinnitus emerged depending on the cue onset timing and duration of the gap-prepulse. Since inhibition deficits were observed in both groups at the same 20-ms gap condition, but with the tinnitus-pitch-non-matched frequency background noise, the present study did not offer proof of concept for tinnitus filling in the gap. Additional studies on the intrinsic effects of different background frequencies on the gap processing are required in the future.