The efficient cell transfection method is vital for various biomedical applications, such as the CRISPR-Cas9 technique. Current cell transfection methods, including lipofectamine, calcium phosphate co-precipitation, nucleofection, and viral infection are not equally efficient for various cells and have their disadvantages. In this study, a magnetic nanoparticle (MNP)-based method was introduced for delivering both FITC dye and a functional EGFP gene into easy-to-transfect HEK cells and difficult-to-transfect rat primary cortical neurons. The transfection efficacy could be controlled in both time-dependent and magnetic strength-dependent manner. This cell transfection method could have substantial potential for targeted drug delivery.