Pain has not only sensory, but also emotional and cognitive, components. Some studies have explored the effect of pain on time perception, but the results remain controversial. Whether individual pain-related emotional and cognitive factors play roles in this process should also be explored. In this study, we investigated the effect of electrical stimulation-induced pain on interval timing using a temporal bisection task. During each task session, subjects received one of five types of stimulation randomly: no stimulus and 100 and 300 ms of non-painful and painful stimulation. Pain-related emotional and cognitive factors were measured using a series of questionnaires. The proportion of "long" judgments of a 1,200-ms visual stimulus duration was significantly smaller with 300 ms painful stimulation than with no stimulus (P < 0.0001) and 100 ms (P < 0.0001) and 300 ms (P = 0.021) non-painful stimulation. The point of subjective equality (PSE) did not differ among sessions, but the average Weber fraction (WF) was higher for painful sessions than for no-stimulus session (P = 0.022). The pain fear score correlated positively with the PSE under 100 ms non-painful (P = 0.031) and painful (P = 0.002) and 300 ms painful (P = 0.006) stimulation. Pain catastrophizing and pain anxiety scores correlated significantly with the WF under no stimulus (P = 0.005) and 100 ms non-painful stimulation (P = 0.027), respectively. These results suggest that electrical stimulation-induced pain affects temporal sensitivity, and that pain-related emotional and cognitive factors are associated with the processing of time perception.