In the delignification process the mass transport of lignin fragments from pits and fibers wall into black liquor is a critical and rate determining step. Hence a detailed study of transport phenomena is essential to have a better understanding of the pulping process. Herein, to study the diffusion of kraft lignin molecules we used diffusion cells with cellulose membranes of different pore sizes. In this setup, diffusion of lignin molecules from the donor chamber to the acceptor chamber through the membrane is determined by concentration measurement. Additionally, size exclusion chromatography (SEC) and UV/Vis absorbance spectra of the donor and acceptor were recorded to determine the molecular weight distribution in both acceptor and donor chambers. A characteristic peak at around 350 nm was observed in the UV/Vis spectra of acceptor solutions. It can be concluded that conjugated molecules in the acceptor side have a higher concentration compared to donor side which is an indication of fractionation based on chemical structure. These results were approved by measurement of molecular weight (Mw) in SEC which show a noticeable difference in donor and acceptor. We interpret these findings as a proof of size fractionation when molecules pass through the pores of membrane. Additionally, SEC data show that the pore size of membrane and molecular size of lignin moieties can result in the change of transport mechanism. In small pore membranes, the diffusion of small individual molecules is enabled while these membranes hinder the transport of lignin clusters.