Mass transport of liberated lignin fragments from pits and fiber walls into black liquor is considered a determining step in the delignification process. However, our current understanding of the diffusion of lignin through cellulose and the influential parameter on this process is very limited. A comprehensive and detailed study of lignin mass transport through cellulosic materials is, therefore, of great importance. In this study, diffusion cell methodology is implemented to systematically investigate the transport of fractionated kraft lignin molecules through model cellulose membranes. Pulping is a complex process and lignin is very heterogenous material therefore to perform a more detailed study on lignin diffusion, we included an additional solvent fractionation step. One of the benefits of this method is that the setup can be adjusted to various experimental conditions allowing the complex chemical reactions occurring during pulping, which would affect the mass transfer of lignin, to be avoided. Here, the effects of the alkalinity of the aqueous solution and molecular weight of the kraft lignin molecules on their diffusion were investigated. Additionally, NMR spectroscopy, size exclusion chromatography, and UV/Vis spectroscopy were used to characterize the starting material and the molecules that passed through the membrane. Lignin molecules detected in the acceptor chamber of the diffusion cells had lower molecular weights, indicating a size fractionation between the donor and acceptor chamber. UV/Vis showed higher concentrations of ionized conjugated kraft lignin molecules in the acceptor chamber, which is a sign of chemical fractionation. This study suggests that the diffusion of lignin through small cellulose pores can be enhanced by decreasing the average molecular weight of the diffusing kraft lignin molecules and increasing alkalinity.