This study aimed to (1) investigate the effect of pulse polarity on neural response of the electrically stimulated cochlear nerve in children with cochlear nerve deficiency (CND) and children with normal-sized cochlear nerves and (2) compare the size of the pulse polarity effect between these two subject groups. The experimental and control group included 31 children with CND and 31 children with normal-sized cochlear nerves, respectively. For each study participant, evoked compound action potential (eCAP) input/output (I/O) functions for anodic-leading and cathodic-leading biphasic stimuli were measured at three electrode locations across the electrode array. The dependent variables of interest included the eCAP amplitude measured at the maximum comfortable level of the anodic stimulus, the lowest level that could evoke an eCAP (i.e., the eCAP threshold), the slope of the eCAP I/O function estimated based on linear regression, the negative-peak (i.e., N1) latency of the eCAP, as well as the size of the pulse polarity effect on these eCAP measurements. Generalized linear mixed effect models were used to compare the eCAP amplitude, the eCAP threshold, the slope of the eCAP I/O function, and the N1 latency evoked by the anodic-leading stimulus with those measured for the cathodic-leading stimulus for children with CND and children with normal-sized cochlear nerves. Generalized linear mixed effect models were also used to compare the size of the pulse polarity effect on the eCAP between these two study groups. The one-tailed Spearman correlation test was used to assess the potential correlation between the pulse phase duration and the difference in N1 latency measured for different pulse polarities. Compared with children who had normal-sized cochlear nerves, children with CND had reduced eCAP amplitudes, elevated eCAP thresholds, flatter eCAP I/O functions, and prolonged N1 latencies. The anodic-leading stimulus led to higher eCAP amplitudes, lower eCAP thresholds, and shorter N1 latencies than the cathodic-leading stimulus in both study groups. Steeper eCAP I/O functions were recorded for the anodic-leading stimulus than those measured for the cathodic-leading stimulus in children with CND, but not in children with normal-sized cochlear nerves. Group differences in the size of the pulse polarity effect on the eCAP amplitude, the eCAP threshold, or the N1 latency were not statistically significant. Similar to the normal-sized cochlear nerve, the hypoplastic cochlear nerve is more sensitive to the anodic-leading than to the cathodic-leading stimulus. Results of this study do not provide sufficient evidence for proving the idea that the pulse polarity effect can provide an indication for local neural health.