Purpose <p>This study aimed (1) to determine the biological basis of the interphase gap (IPG) effect and (2) to identify the most informative parameters, analytical methods, and quantitative scales for evaluating the IPG effect in human cochlear implant (CI) users.</p> Methods <p>The IPG effect was quantified using multiple parameters, analytical methods, and quantitative scales (three combinations using linear or logarithmic scales for the input and output variables) across three pediatric CI groups with differing cochlear nerve (CN) anatomy: children with cochlear nerve deficiency (CND), GJB2 mutations, and idiopathic sensorineural hearing loss (SNHL). All participants in the GJB2 and idiopathic SNHL groups had normal-sized CNs (NSCNs) in the test ear. Neural synchrony, a property depending on neural health, was assessed using phase locking value (PLV) and compared between children with CND and those with GJB2 mutations.</p> Results <p>The PLV did not differ significantly between the CND and GJB2 groups, nor did it correlate with the IPG effect in GJB2 cases, regardless of parameter, analytical method, or quantitative scale. In contrast, consistent group differences in IPG effects on stimulation level offset and maximum slope of the eCAP input/output function were observed across all analytical methods and quantitative scales. The sensitivity of other eCAP measures—threshold, maximum amplitude, and overall linear slope—to group differences varied by quantitative scale.</p> Conclusions <p>The IPG effect primarily reflects the number of active CN fibers rather than their health. Stimulation level offset and the IPG effect on maximum slope are robust indicators of CN fiber counts in CI users and are unaffected by the choice of quantitative scale.</p>