Background: There is a huge controversy about whether xenograft or allograft in the “immune-privileged” brain needs immunosuppression. In animal studies, prevailing sophiscated immunosuppression or immunodeficiency is detrimental for the recipients, which results in short lifespan of animals, and confounds functional behavioral readout of the graft benefit, discouraging long-term follow-up. Methods: Neuron-restricted human neural progenitor cells (NPCs) were derived from human embryonic stem cells (ESCs, including H1, its gene-modified cell lines for better visualization, and HN4), propagated for different passages and then transplanted into the brain of immunocompetent rats without use of immunosuppressant. The graft survivals, their cell fates and HLA expression levels were examined over time (up to months after transplantation). We compared the survival capability of NPCs from different passages, and in different transplantation sites (brain parenchyma vs. para-and intra-ventricular sites). The host responses to the grafts were also investigated.Results: Our results show that human ESC-derived neuron-restricted NPCs survive extendedly in adult rat cerebro-parenchyma with no need of immunosuppression whereas a late-onset graft rejection seems inevitable. Both donor HLA expression level and host MHC-II expression level remain relatively low and little change over the long-term survival, and therefore can’t predict the late-onset rejection. Human grafts in or close to cerebroventricle are more vulnerable to the immune attack than the intra-striatum grafts. Prevention of graft hyperplasia by using hypoproliferative late-passaged human NPCs further significantly extends the graft survival time. Our new data also shows that a subpopulation of host microglia upregulate MHC-II expression in response to the human graft, but fail to present the human antigen to the host immune system, suggestive of the immune-isolation role of the blood–brain barrier (BBB). Conclusions: The present study confirms the “immune privilege” of the brain parenchyma, and more importantly, unveils that choosing hypoproliferative NPCs for transplantation can benefit graft outcome in terms of both lower tumor-genic risk and the prolonged survival time without immunosuppression.