Fluid and HCO₃⁻ secretion are vital functions of the pancreatic duct and other secretory epithelia. CFTR and Cl⁻/HCO₃⁻ exchange activity at the luminal membrane are required for these functions. The molecular identity of the Cl⁻/HCO₃⁻ exchangers and their relationship with CFTR in determining fluid and HCO₃⁻ secretion are not known. We show here that the Cl⁻/HCO₃⁻ exchanger slc26a6 controls CFTR activity and ductal fluid and HCO₃⁻ secretion. Unexpectedly, deletion of slc26a6 in mice and measurement of fluid and HCO₃⁻ secretion into sealed intralobular pancreatic ducts revealed that deletion of slc26a6 enhanced spontaneous and decreased stimulated secretion. Remarkably, inhibition of CFTR activity with CFTR_inh‐172, knock‐down of CFTR by siRNA and measurement of CFTR current in WT and slc26a6^−/− duct cells revealed that deletion of slc26a6 resulted in dis‐regulation of CFTR activity by removal of tonic inhibition of CFTR by slc26a6. These findings reveal the intricate regulation of CFTR activity by slc26a6 in both the resting and stimulated states and the essential role of slc26a6 in pancreatic HCO₃⁻ secretion in vivo.