Background: Stem cells have created hope for treatment of obstinate cases as injured spinal cord (ISC). Objective: aims to assess possible early therapeutic effect of bone marrow mesenchymal stem cells (BM-MSCs) on regeneration of ISC and to estimate effective transplantation routes in animal models. Material and Methods: 62 adult male albino rats were used; two rats for BM-MSCs extraction and 60 rats were allocated into three groups. Control group: subjected to ISC, intralesional (IL) group: injected with BM-MSCs via intralesional injection and intravenous (IV) group: injected with BM-MSCs via intravenous injection at 3rd day post cord injury (PCI). Rats were examined to assess motor functional recovery. SC specimens were extracted for histological, morphometric, chemical, Immunological and statistical studies. Results: Tracing BM-SCs of SC, (IL) group versus (IV) group showed higher number of engrafted stem cells at all studied ages with gradual decrease from 1st to 6th week PCI. The MSCs counts in (IL) versus (IV) groups were highly significantly increased at 1st, 3rd weeks but only significantly increased at 6th week. They were concentrated at injury site of SC in (IL) group then extended out rostrally and caudally. In (IV) group, they were dispersed over wider area including injury site indicating their capability to "home". The mean cavitation areas in treated versus control groups showed highly significant decrease and the smallest cavitation areas observed were in (IL) group. Also (IL) group showed highest neurotrophic factors expressions than other groups with increasing pattern from 1st to 3rd week then decreased at 6th week. Locomotor recovery scores in treated versus control groups showed highly significant increase with highest improvement in (IV) group. Conclusion: This work concluded that early transplantation of BM-MSCs in ISC gave outstanding improvement. Intravenous route therapy provided highest locomotor recovery while intralesional route gave best histological and neuroprotective outcomes.