PVDF membranes are extensively applied in ultrafiltration processes of aqueous solutions of different chemical substances owing to its outstanding properties, such as high mechanical strength, thermal stability, and chemical resistance. However, hydrophobicity of this polymer largely limits the practical application of PVDF. Therefore, it is very important to develop methods of modifying the surface of PVDF membranes with the aim to improve their properties. Polyethyleneimine, as a modifying agent, has already been investigated for hydrophilization of the surface. However, the modification process leads to reduction of the volumetric flow and changes of the membrane selectivity because polymer is grafted not only to the surface, but also into the pores of the membranes, reducing their effective radius. Taking everything into account, this investigation is devoted to the development of a technique for surface modification of PVDF membranes with PEI (with pre-filling of pores) to improve their transport properties, at the same time preserving the morphology of the membrane and its characteristics. Nonionic surfactant Tetronic® 701 is used as a pore-filling agent. Commercial ultrafiltration PVDF membranes (with cut-off of 150 kDa) were firstly activated with a carbonate buffer, then the pores were filled with Tetronic® 701, further surface modification of membranes with PEI was performed. The modification process was confirmed by IR spectroscopy. The surface properties of the membranes were studied by scanning electron microscopy. The changes in the hydrophilicity of the modified membranes were studied by measuring the wetting angles of the membrane surface with water, glycerol, and diiodomethane. The transport properties of the membrane were experimentally studied in the process of ultrafiltration of aqueous protein solution (in particular, lysozyme, lipase, BSA); water permeability coefficients and protein rejection coefficients were determined. It was found that the usage of Tetronic® 701 during the membrane modification process allowed improving the water permeability coefficient compared to the membrane modified without pre-filling the pores; hydrophilization of the surface reduced the effect of concentration polarization.