This study analyzes the varying electrophoretic mobility and zeta potential of bone marrow stromal cells (BMSCs) during their differentiation towards neurons. Electrophoresis of primary BMSCs and neuron growth factor (NGF)-induced neuron-like cells with the uptake of heparin-functionalized poly(lactide-co-glycolide) (PLGA) nanoparticles (NPs) are also investigated. Immunofluorescent images revealed fiat a high concentration of NGF accelerated the differentiation of BMSCs into neurons. When the concentration of NGF increased, the absolute values of electrophoretic mobility and zeta potential of the differentiating BMSCs increased. In addition, a longer inductive period yielded higher charge of the differentiating BMSCs and a smaller uptake amount of heparin-functionalized PLGA NPs. However, an increase in the loading efficiency of heparin on PLGA NPs enhanced the uptake and reduced the electrical characteristics of the primary and differentiating BMSCs. Hence, a general rule is drawn that an increase in the uptake of heparin-functionalized PLGA NPs decreased the electrophoretic mobility and zeta potential of BMSCs during differentiation towards neurons.