The canonical Wnt–β-catenin signaling pathway is initiated by inducing phosphorylation of one of the Wnt receptors, low-density lipoprotein receptor-related protein 6 (LRP6), at threonine residue 1479 (Thr¹⁴⁷⁹) and serine residue 1490 (Ser¹⁴⁹⁰). By screening a human kinase small interfering RNA library, we identified phosphatidylinositol 4-kinase type II α and phosphatidylinositol-4-phosphate 5-kinase type I (PIP5KI) as required for Wnt3a-induced LRP6 phosphorylation at Ser¹⁴⁹⁰ in mammalian cells and confirmed that these kinases are important for Wnt signaling in Xenopus embryos. Wnt3a stimulates the formation of phosphatidylinositol 4,5-bisphosphates [PtdIns (4,5)P₂] through frizzled and dishevelled, the latter of which directly interacted with and activated PIP5KI. In turn, PtdIns (4,5)P₂ regulated phosphorylation of LRP6 at Thr¹⁴⁷⁹ and Ser¹⁴⁹⁰. Therefore, our study reveals a signaling mechanism for Wnt to regulate LRP6 phosphorylation.