Abstract Background The FGF and Wnt pathways have been implicated in gonadotropin-releasing hormone (GnRH) deficiency, but their crosstalk during human GnRH neuron ontogeny remains unexplored. Methods GnRH neurons were differentiated from human pluripotent stem cells (hPSCs) by combining Wnt and dual SMAD inhibition for 10 days, followed by temporally-controlled FGFR1 depletion for 10–20 days using an auxin-inducible degron system. FGF8b stimulation and FGF8 blocking were tested. Transcriptomic changes in neural progenitor cells (NPCs) and GnRH neurons were examined using bulk RNA-sequencing. Results Early Wnt inhibition induced GnRH neuron formation without exogenous FGF8b, possibly by upregulating anterior forebrain markers and endogenous FGF8 in NPCs. Blocking this endogenous FGF8 diminished GnRH neuron formation. FGFR1 depletion in NPCs suppressed FGF8 expression, and neuron GnRH decapeptide secretion and GNRH1 expression. GNRH1 expression was rescued by FGF8b treatment. Conclusions Early Wnt inhibition promotes human GnRH neuron development through FGFR1-mediated FGF8 signaling. These findings advance the understanding of the complexity of FGF8-FGFR1 pathway interactions and their role in olfactory and hypothalamic neuron differentiation, particularly in GnRH neuron ontogeny.