The aim of this research was to use theoretical data and experimental procedures to determine permeate flux’s dependence on time during cross-flow filtration combined with the use of backwashing using permeate in bioparticle separation, specifically in blood filtration. A method that reduces filter membrane fouling for the first stage of blood filtration (plasmapheresis) in an implantable artificial kidney is proposed. The proposed method uses the body’s internal energy (blood pressure pulsation) to provide enough movement for the diaphragm pump to make reverse flow as a backwash flow for reducing membrane fouling. The test conditions, which mimicked the human cardiovascular system, were provided by a cardiovascular pump and a hospital monitoring system. The results demonstrate that the membrane backwashing can maintain the permeate flux at a level that is nearly three times higher than the long-term flux without membrane backwashing. The effects of operating parameters such as cross-flow velocity, Womersley number, pressure difference, and filtration time on permeate flux were experimentally investigated. A correlation of the flux to shear rate for frequencies less than 2 Hz (heartbeat of 120 beats per minute) was developed and the results were compared with those obtained using cross-flow filtration techniques.