Non‐specific phospholipase C (NPC) is involved in plant growth, development and stress responses. To elucidate the mechanism by which NPCs mediate cellular functions, here we show that NPC4 is S‐acylated at the C terminus and that acylation determines its plasma membrane (PM) association and function. The acylation of NPC4 was detected using NPC4 isolated from Arabidopsis and reconstituted in vitro. The C‐terminal Cys‐533 was identified as the S‐acylation residue, and the mutation of Cys‐533 to Ala‐533 in NPC4 (NPC4C533A) led to the loss of S‐acylation and membrane association of NPC4. The knockout of NPC4 impeded the phosphate deficiency‐induced decrease of the phosphosphingolipid glycosyl inositol phosphoryl ceramide (GIPC), but introducing NPC4C533A to npc4‐1 failed to complement this defect, thereby supporting the hypothesis that the non‐acylated NPC4C533A fails to hydrolyze GIPC during phosphate deprivation. Moreover, NPC4C533A failed to complement the primary root growth in npc4‐1 under stress. In addition, NPC4 in Brassica napus was S‐acylated and mutation of the S‐acylating cysteine residue of BnaC01.NPC4 led to the loss of S‐acylation and its membrane association. Together, our results reveal that S‐acylation of NPC4 in the C terminus is conserved and required for its membrane association, phosphosphingolipid hydrolysis and function in plant stress responses.