Abstract The objective of the present study was to produce an endo-polyglacturonase by Wickerhanomyces anomalus, in a low cost fermentation medium, by batch and fed-batch cultures in order to be used in the enzyme. The effect of several nutrients on PGase production, were evaluate at shakes flasks, in a reference fermentation medium, using one factor at a time method, Plackett-Burman design and response surface methodology. The optimized fermentation medium was used to evaluate the growth and production of the enzyme by batch and fed-batch cultures, at a lab scale bioreactor. PGase activity obtained in the RF medium was ∼20 U/mL. The absence of trace element solution had a repressive effect on the enzyme synthesis. The addition of yeast extract, instead of vitamins and amino acids, in the culture medium, improved the production of the enzyme. Plackett-Burman design determined that only pectin and yeast extract had significant and positive effect on PGase production. The Doehlert design determined that maximum PGase synthesis was obtained with 6.0 and 0.8 g/L of pectin and yeast extract, respectively. The final optimized fermentation medium included glucose, pectin, urea, yeast extract and salts. In this medium, PGase synthesis reached ∼25 U/mL, and ∼49 U/mL, in batch and fed-batch cultures, respectively, at lab scale bioreactor. In this study, it was able to obtain enzymatic extract with high PGase activity, by the growth of W. anomalus in a low cost culture medium, by fed-batch system, for its future use in the enzymatic cassava starch extraction.