A crucial step in the chemical delignification of wood is the transport of lignin fragments into free liquor; this step is believed to be the rate-limiting step. This study has investigated the diffusion of kraft lignin molecules through model cellulose membranes of various pore sizes (1–200 nm) by diffusion cells, where the lignin molecules diffuse from donor to acceptor cells through a membrane, where diffusion rate increases by pore size. UV–vis spectra of the donor solutions showed greater absorbance at higher wavelengths (~450 nm), which was probably induced by scattering due to presence of large molecules/clusters, while acceptor samples passed through small pore membranes did not. The UV–vis spectra of acceptor solutions show a characteristic peak at around 350 nm, which corresponds to ionized conjugated molecules: indicating that a chemical fractionation has occurred. Size exclusion chromatography (SEC) showed a difference in the molecular weight (Mw) distribution between lignin from the donor and acceptor chambers. The results show that small pore sizes enable the diffusion of small individual molecules and hinder the transport of large lignin molecules or possible lignin clusters. This study provides more detail in understanding the mass transfer events of pulping processes.