FePt nanoparticles (NPs) have recently been revealed to be significant multifunctional materials for the applications of biomedical imaging, drug delivery and magnetic hyperthermia due to their novel magnetic properties. In this study, a newly discovered photothermal effect activated by the near infrared (NIR) femtosecond laser for FePt NPs was demonstrated. The threshold laser energy to destroy cancer cells was found to be comparable to that of gold nanorods (Au NRs) previously reported. Through the thermal lens technique, it was concluded that the temperature of the FePt NPs can be heated up to a couple of hundreds degree C in picoseconds under laser irradiation due to the excellent photothermal transduction efficiency of FePt NPs. This finding boosts FePt NPs versatility in multifunctional targeted cancer therapy.