Our previous study found that ectomesenchymal stem cells derived from human pluripotent stem cells (hPSC-EMSCs) exhibited higher neuroprotective potential than hUC-MSCs, as evidenced by a more significant reduction in lesion size and apoptosis in rat brains after hypoxia-ischemia (HI). Moreover, in vitro studies demonstrated that hPSC-EMSC-derived conditioned medium (CM) had neuroprotective and neurorestorative effects through the promotion of anti-apoptosis, neurite growth and neurogenesis. In this study, we discovered that hPSC-EMSCs and hUC-MSCs expressed differential secreted factors by utilizing RNA-seq, MASS-SPEC and enzyme-linked immunosorbent assay. Direct comparison between hPSC-EMSCs and hUC-MSCs revealed a significant enrichment of a panel of secreted factors, including nerve growth factor (NGF), platelet-derived growth factor-AA, and transforming growth factor-β2, in hPSC-EMSCs. These factors play essential roles in neurogenesis, synaptic transmission and neurotransmitter transport. Mechanistically, hPSC-EMSC-derived CM enhanced NGF-induced neurite outgrowth and neuronal differentiation of NPCs via the ERK/CREB pathway. Inhibition of ERK or CREB abolished CM-enhanced neurogenesis and neurite outgrowth. Finally, we found that intranasal delivery of the CM derived from hPSC-EMSCs significantly reduced brain lesion size, promoted endogenous neurogenesis, mitigated inflammatory responses and improved functional recovery in rats with HIE. Collectively, we conclude that hPSC-EMSCs promote functional recovery after HI through multifaceted neuromodulatory activities via paracrine/trophic mechanisms.