Phosphatidylinositol 4-kinase alpha (PI4KA) is an essential lipid kinase that generates phosphatidylinositol 4-phosphate (PI4P) from phosphatidylinositol (PI) at the plasma membrane (PM). PI4P is a precursor for PIP2 and PIP3 lipid signalling, with PI4P serving a critical role in maintaining PM identity and asymmetry. Given the important roles of PI4KA in myriad processes, understanding how it is regulated is of immense importance. Here, we have identified that PI4KA can be phosphorylated in its dimerization domain (pY1154) and kinase domain (pY2090) by a cohort of tyrosine kinases. Phosphorylation of pY2090 significantly impairs lipid kinase activity of PI4KA but does not alter its recruitment to membranes by its regulatory protein EFR3. Cryo-EM and HDX-MS analysis reveals that phosphorylation does not result in dramatic conformational changes but instead causes localised changes in the ka12 C-terminal helix of PI4KA. Phosphorylation of the C-terminal helix is found in multiple PI3Ks and PI4Ks, suggesting this may be a evolutionarily conserved regulatory mechanism. Overall, our work reveals a novel regulatory mechanism for PI4KA that directly alters its lipid kinase activity.