The selective separation of biomolecules is a critical process in food, biomedical and pharmaceutical industries. Due to its size and properties, mesoporous silica offers many advantages as a separation media for biomolecules such as proteins and enzymes. In this paper, we investigate mathematically the separation of proteins trypsin and lysozyme using mesoporous silica materials. These proteins are modelled as densely packed spheres, while the silica pore is assumed to have a cylindrical structure. The Lennard–Jones potential together with a continuum approximation is employed to determine the interaction among the proteins and the interaction between a protein and a silica pore. For these systems, the total interaction energies are obtained analytically as functions of the protein size and the pore dimensions. We find that the pore radii which give rise to the maximum adsorption energies for trypsin and lysozyme are 21.74 Å and 17.74 Å, respectively. Since the binding energy between any two protein molecules is found to be three orders of magnitude lower than the adsorption energy of the protein into the silica pore, proteins prefer to be separated and stay inside the pore. Further, we find that using silica pores with radii in the range between 17.23 Å and 21.24 Å allows the entrance of only lysozyme, as such separating lysozyme from trypsin. These results agree with previous experimental study, confirming that mesoporous silica pores may be used to separate trypsin–lysozyme mixture.