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It is known that a charge is generated in water and protein solutions upon their motion; this phenomenon is also observed in analytical systems for atomic force microscopy (AFM)-based fishing. At that, the efficiency of protein fishing correlates with the value of charge, generated upon the motion of the analyzed solution. Earlier, we demonstrated that a pulsed electric field can well be used for the enhancement of the efficiency of AFM-based fishing of low-abundant protein. In this paper, we have demonstrated the influence of a pulsed electric field on the stimulation of the electric charge generation in a solution of low-abundant proteins observed in the injector part of an AFM-based fishing system at 23 °C and 38 °C. Taking this effect into account is important for the development of novel highly sensitive flow-based diagnostic systems, as well as for the development of models describing the influence of a pulsed electric field on pathological processes in the body, hemodynamics, and physicochemical properties of solutions.