Abstract Background Epilepsy is one of the most common and serious brain conditions, characterised by recurrent unprovoked seizures. It affects about 1% of the population worldwide. Despite a range of antiepileptic drugs being available, one third of the patients do not achieve adequate seizure control. Only a minority of these patients may be suitable to undergo surgical resection of the seizure focus, but this is an invasive and not always successful procedure. There is an urgent need to develop more effective treatment options for uncontrolled seizures. With the recent advances in regenerative and translational medicine, cell therapies could prove to be beneficial. Here we describe the protocol for a proposed systematic review and meta-analysis to assess the effects for cell transplantation in animal models of epilepsy. Methods We will include all preclinical animal models of epilepsy that evaluate the effects of cell transplantation compared to the untreated control. The primary outcome will be the change in frequency and duration of seizures from baseline measured by video electroencephalography (EEG). The secondary outcomes will include histological and neurobehavioural assessments. We will perform an electronic search of MEDLINE via PubMed, Web of Science, and EMBASE. Search results will be screened independently by two reviewers and confirmed by a third reviewer. Data from eligible studies will be extracted and pooled, and the summary estimate of effect size will be calculated using DerSimonian and Laird random effects meta-analysis. Heterogeneity will be explored using sub-group meta-analysis, and meta-regression risk of bias will be assessed by using the CAMARADES checklist for study quality tool. Discussion The purpose of this systematic review is to assess and summarise the existing literature in the field of cell transplantation as a treatment for epilepsy in animal models. Efficacy will be measured by evaluating the reduction in seizure intervals, number, and duration, within animal models of epilepsy. Analysis of the existing literature will mark the achievement made in the field and locate the existing gaps, a process that will aid in the search for the next needed step. Systematic review registration CRD42018103628