This study demonstrates the feasibility of layer-by-layer (LbL) assembly of poly(sodium 4-styrene sulfonate) (PSS)/poly(diallyldimethylammonium chloride) (PDADMAC) polyelectrolyte multilayers on an anion exchange membrane (AEM). The electrodeposition of (PSS/ PDADMAC)(n) multilayers on the AEM with a PSS layer as the top surface endows the surface with negative charges and increases the surface hydrophilicity, leading to a significantly improved antifouling performance in electrodialysis (ED) to an organic foulant, i.e., sodium dodecyl sulfate (SDS). The desalination rate during 180 min increased from 24.0% for the pristine AEM to 30.5% for a 5.5 PSS/ PDADMAC bilayers modified AEM with 75 mg/L SDS in the initial solution. A SDS fouling layer was formed at the dilute side of the pristine AEM, causing a sharp increase of electrical resistance and restricting the ion transport through the AEM completely. Electrodeposition of 5.5 PSS/ PDADMAC bilayers prevented the formation of the SDS fouling layer at the surface of AEM, which reduced the sharp increase of electrical resistance and kept the ion transport through the AEM unaffected. With 100 or 150 mg/L SDS in the initial solution, the desalination rate during 180 min increased from 24.1% or 15.4% for the pristine AEM to 28.4% or 26.8% for the 5.5 PSS/ PDADMAC bilayers modified AEM.