OBJECTIVE A period of unilateral implant use before bilateral implantation affects timing of brainstem processes measured by the electrically evoked auditory brainstem response (EABR). BACKGROUND EABR latencies decrease with unilateral implant use potentially disrupting binaural timing cues important in auditory brainstem processing of bilateral input. METHODS EABRs were evoked by electrical pulses from the left, right, and both implants simultaneously in 3 groups of children. All were initially implanted at ages younger than 3 years and had the following: 1) a long delay (>2 yr [n = 16]), 2) a short delay (<1 yr [n = 15]), or 3) no delay (n = 15) between left and right ear implantation. Responses were recorded on the first day of bilateral implant use and 3 and 9 months thereafter. RESULTS Relative to responses evoked in the experienced ear, the naive ear showed prolonged latency in both the EABR peaks and the binaural difference response. After 3 and 9 months of bilateral implant use, the relative prolongation decreased in the long and short delay groups, but significant differences persisted in the former. No clear differences in latencies evoked by the left versus right implant were found at any time point in children receiving bilateral implants simultaneously. CONCLUSIONS Results suggest potential disruptions to binaural brainstem processing based on timing cues in children receiving a second cochlear implant after more than 2 years of unilateral implant use that persist through at least the first 9 months of bilateral implant use.