Guanylate cyclase 2C (GCC), a receptor for bacterial heat-stable enterotoxin ST on the apical intestinal epithelium, generates cGMP and causes excessive intestinal secretion leading to diarrhea upon activation. This study reports that the C-terminal PSD95, Dlg1, ZO-1 (PDZ) domain interacting motif in GCC interacts with scaffolding proteins sodium-hydrogen exchanger regulatory factor (NHERF)1–4. NHERF4 binding inhibits GCC catalytic activity, unlike NHERF1, 2, and 3. The inhibition of GCC activity was mimicked by two synergistically acting NHERF4 peptides (N4-110 [NH2-LERPRFCLL-COOH] and N4-195 [NH2-RHAHDVARAQLG-COOH]), peptides with high sequence homology to the GCC catalytic domain. In native NHERF4, these peptides are in close spatial proximity to each other within the PDZ domain. Based on 3-D guanylate cyclase domain modeling, the binding sites for N4-110 and N4-195 were both mapped to the GCC dimer interface. FRET analysis confirmed that NHERF4 PDZ1 domain binding interferes with GCC oligomerization. Studies in murine and human enteroid models showed that NHERF4 binding and inhibition of GCC activity are enhanced by excessive GCC activation following ST stimulation. This suggests NHERF4 inhibits unregulated GCC activity in diarrhea. Overall, our findings reveal a novel regulatory mechanism of GCC, offering insights for developing new therapies for enterotoxin-triggered diarrheas.