Background: Nose reference (NR), mastoid reference (MR), and montage average reference (MAR) are usually used in auditory event-related potential (AEP) studies with a recently developed reference electrode standardization technique (REST), which may reduce the reference effect. For children with cochlear implants (CIs), auditory deprivation may hinder normal development of the auditory cortex, and the reference effect may be different between CIs and a normal developing group.Methods: Thirteen right-side-CI children were recruited, comprising 7 males and 6 females, ages 2–5 years, with CI usage of ~1 year. Eleven sex- and age-matched healthy children were recruited for normal controls; 1,000 Hz pure tone evoked AEPs were recorded, and the data were re-referenced to NR, left mastoid reference (LMR, which is the opposite side of the implanted cochlear), MAR, and REST. CI artifact and P1–N1 complex (latency, amplitudes) at Fz were analyzed.Results: Confirmed P1–N1 complex could be found in Fz using NR, LMR, MAR, and REST with a 128-electrode scalp. P1 amplitude was larger using LMR than MAR and NR, while no statistically significant difference was found between NR and MAR in the CI group; REST had no significant difference with the three other references. In the control group, no statistically significant difference was found with different references. Group difference of P1 amplitude could be found when using MR, MAR, and REST. For P1 latency, no significant difference among the four references was shown, whether in the CI or control group. Group difference in P1 latency could be found in MR and MAR. N1 amplitude in LMR was significantly lower than NR and MAR in the control group. LMR, MAR, and REST could distinguish the difference in the N1 amplitude between the CI and control group. Contralateral MR or MAR was found to be better in differentiating CI children versus controls. No group difference was found for the artifact component.Conclusions: Different references for AEP studies do not affect the CI artifact. In addition, contralateral MR is preferable for P1–N1 component studies involving CI children, as well as methodology-like studies.