The ability of a charged UF membrane to fractionate the small peptides found in a rapeseed protein enzymatic hydrolysate, according to their charge characteristics, was investigated. The complexity of such a hydrolysate has required the setting up of technological alternatives to isolate the small peptides, to obtain a more efficient separation among the numerous peptide species. A preliminary step consisted of precipitation followed by filtration with a 3000 g/mol molecular weight cutoff (MWCO) membrane to obtain a solution concentrated in small peptides. The possibility of fractionating these small peptides by a charged 1000 g/mol MWCO membrane was investigated. The study enabled us to assess the contribution of electrostatic interactions during fractionation. The effect of pH and ionic strength on the peptide transmission was studied. The ionic strength contribution was considered by studying the effect on the selectivity of a desalting step by nanofiltration on a 500 g/mol MWCO membrane. Peptide transmission was lower at pH 9 than pH 4, and it was the lowest at pH 9 and low ionic strength. Ionic strength had a significant influence at pH 9 but showed no influence at pH 4. The amino acid analysis and capillary electrophoresis revealed that negatively charged (acid) peptides were found in lower proportions in the permeate. The opposite trend was observed for basic peptides, whereas neutral peptides were found in the same proportion in the retentate and the permeate. These results can be explained, according to the Donnan theory, by the existence of attractive and repulsive forces at the membrane-solution interface. Selectivity between basic and acid peptides was as high as 1.90 at pH 9 and low ionic strength. A rough sketch of a membrane-based process is proposed to fractionate rapeseed peptide mixtures. Results obtained were reproducible within 10%.