We develop a PCR method utilizing carbon-coated iron (Fe@C) nanoparticles. The outer carbon layers of the nanoparticles absorb near-infrared (NIR) light and release energy as heat. We carry out PCR performing thermal cycling via the on/off operation of NIR irradiation to the nanoparticles. We show that the total time of PCR is shortened compared to the conventional method thanks to rapid, efficient heating by Fe@C nanoparticles. We also show that the amount of by-products is smaller than the conventional case, which may be attributed to the rapid thermal cycling.