To improve the efficiency of poly (D, L-lactic-co-glycolic acid) (PLGA) nanoparticles (NP) as a gene carrier for the transfection of human mesenchymal stem cells (hMSCs), we developed a light-emitting diode (LED)-induced gene delivery system. The size of NP produced at various LED wavelengths (blue, green, red, and NIR) was controlled in the colloidal state (a mixture of single particles and agglomerates). In addition, physical stimulation of cell membranes using two LED wavelengths (blue and near infrared (NIR)) altered their structure and facilitated the penetration of cells with extracellular substances. The reduction of NP size and increase in cell membrane permeability effectively increased gene delivery to cells and protein expression by improving transfection processes (cellular uptake, endosomal escape, and PEI-gene dissociation). The effects of 10 min irradiation at each LED wavelength were compared with those of the non-irradiated sample. The reduction of NP size by LED irradiation was confirmed using DLS, SEM, and Nanosight, and cell membrane permeability was assessed by confocal laser microscopy and FACS. Transfection efficiency was measured using confocal laser microscopy, FACS, and Western blot analysis. Among the tested LED wavelengths, NIR light irradiation was the most effective in reducing NP size and increasing cell membrane permeability. Conversely, blue light irradiation significantly increased gene delivery to cells by accelerating transfection processes. Thus, the LED-irradiation mediated NP dispersion method improved the delivery efficiency of PLGA NP as gene carrier, and by enhancing cell membrane permeability, extracellular substances that normally cannot easily penetrate the cell membrane were delivered in a timely and effective manner.