Cochlear implant (CI) users can derive a musical pitch from the temporal pattern of pulses delivered to one electrode. However, pitch perception deteriorates with increasing pulse rate, and most listeners cannot detect increases in pulse rate beyond about 300 pps. In addition, previous studies using irregular pulse trains suggest that pitch can be substantially influenced by neural refractory effects. We presented electric pulse trains to one CI electrode and measured rate discrimination, pitch perception, and auditory nerve (AN) activity in the same subjects and with the same stimuli. The measures of AN activity, obtained using the electrically evoked compound action potential (ECAP), replicated the well-known finding that the neural response to isochronous pulse trains at rates above about 200-300 pps is modulated, with the ECAP being larger to odd-numbered than to even-numbered pulses. This finding has been attributed to refractoriness. Behavioural results replicated the deterioration in rate discrimination at rates above 200-300 pps and the finding that pulse trains whose inter-pulse intervals (IPIs) alternate between a shorter and a longer value (e.g. 4 and 6 ms) have a pitch lower than that corresponding to the mean IPI. To link ECAP modulation to pitch, we physically modulated a 200-pps pulse train by attenuating every other pulse and measured both ECAPs and pitch as a function of modulation depth. Our results show that important aspects of temporal pitch perception cannot be explained in terms of the AN response, at least as measured by ECAPs, and suggest that pitch is influenced by refractory effects occurring central to the AN.