The non-canonical Wnt/Ca2+ signaling pathway plays important roles in embryonic development, tissue formation and diseases. However, it is unclear how the Wnt ligand-stimulated, G protein-coupled receptor Frizzled activates Phospholipases for calcium release. We report that the zebrafish/human phosphatidylinositol transfer protein Sec14l3/SEC14L2 act as GTPase proteins to transduce Wnt signals from Frizzled to phospholipase C (PLC). Depletion of Sec14l3 attenuates Wnt/Ca2+ responsive activity and causes convergent and extension (CE) defects in zebrafish embryos. Mechanistically, Sec14l3-GDP forms complex with Frizzled and Dishevelled; Wnt ligand binding of Frizzled activates Sec14l3 on the plasma membrane and the resulted Sec14l3-GTP binds to and activates phospholipase Cδ4a (Plcδ4a); Subsequently, Plcδ4a tethers and cleaves phosphatidylinositol-4,5-bisphosphate (PIP2) into diacylglycerol (DAG) and inositol 1,4,5-triphosphate (InsP3), ultimately stimulating calcium release. Furthermore, Plcδ4a can act as a GTPase-activating protein to accelerate the hydrolysis of Sec14l3-bound GTP to GDP. Our data provide a new insight into GTPase protein coupled Wnt/Ca2+ signaling transduction.