The aim of the present study was to investigate the application of two new pitch perception tests in children with cochlear implants (CI) and to compare CI outcomes to normal hearing (NH) children, as well as investigating the effect of chronological age on performance. The tests were believed to be linked to the availability of Temporal Fine Structure (TFS) cues. 20 profoundly deaf children with CI (5-17 years) and 31 NH peers participated in the study. Harmonic Intonation (HI) and Disharmonic Intonation (DI) tests were used to measure low-frequency pitch perception. HI/DI outcomes were found poorer in children with CI. CI and NH groups showed a statistically significant difference (p < 0.001). HI scores were better than those of DI test (p < 0.001). Chronological age had a significant effect on DI performance in NH group (p < 0.05); children under the age of 8.5 years showed larger inter-subject-variability; however, the majority of NH children showed outcomes that were considered normal at adult-level. For the DI test, bimodal listeners had better performance than when listening with CI alone. HI/DI tests were applicable as clinical tools in the pediatric population. The majority of CI users showed abnormal outcomes on both tests confirming poor TFS processing in the hearing-impaired population. Findings indicated that the DI test provided more differential low-frequency pitch perception outcomes in that it reflected phase locking and TFS processing capacities of the ear, whereas HI test provided information of its place coding capacity as well.