Lately, interest has emerged in biorefineries that use non-food biomass residues. Lignin is a lignocellulosic biomass which can be extracted from a residual stream, called black liquor, in the Kraft pulping process and converted to a variety of value-added products. A recent study was carried out to acidify the black liquor and extract the lignin by means of electrodialysis with bipolar membrane (EDBM) method. Despite the fact that this green pathway enjoyed an in-situ production of caustic soda as a valuable byproduct and significantly reduced the chemical consumption than the chemical acidification approach, the occurrence of severe colloidal fouling on the cation exchange layer of the bipolar membrane impaired its productivity. To resolve this obstacle, this investigation was performed to determine, for the first time, the impact of the non-stationary pulsed electric field on mitigation of bipolar membrane colloidal fouling and improvement of the process performance in terms of current efficiency, energy consumption and membrane integrity. A comparison between the experimental results obtained from four pause lapses (6, 12, 18 and 24 s) with a pulse lapse of 6 s and a DC current indicated that application of a rigorous selected pulse/pause ratio can limit the growth of the colloidal particle, suppress the fouling on the bipolar membrane and intensify the EDBM process. The pulse/pause ratio of 6(s)/24(s) was found to be the most appropriate ratio which yielded a high current efficiency (similar or equal to 80%), a low global system resistance and relative energy consumption (2.6 Wh/g - NaOH) and a final pH value of 9.7 which would facilitate an efficient lignin extraction process.