For the synthesis of biocompatible photothermal agents, gold nanorod-embedded polymeric nanoparticles (GPNs) were synthesized using a nanoprecipitation method. Uniform gold nanorods (GNRs), which are sensitive to a photothermal effect by near-infrared (NIR) light, with an aspect ratio of 4.0 were synthesized by a seed-mediated growth method. The hydroxyl groups of polycaprolactone diol (PCL diOH) were modified by esterification with mercaptopropionic acid to give a dithiol (polycaprolactone dithiol, PCL diSH) as a phase transfer and capping agent. Subsequently, hexadecyltrimethylammonium bromide (CTAB), a stabilizer of GNRs, was exchanged and/or removed by PCL diSH. PCL diSH-coated GNRs were further wrapped in a hydrophilic polymer, Pluronic F127, as a stabilizer. These newly formulated GPNs exhibit excellent stability in water and a maximum absorbance in the NIR region indicating a highly efficient surface plasmon resonance effect, phenomena useful for photothermal agents.