The spatiotemporal temperature distributions of NIR irradiated polypyrrole nanoparticles (PPN) were evaluated by varying PPN concentrations and the pH of suspensions. The PPN were synthesized by oxidative chemical polymerization, resulting in a hydrodynamic diameter of 98 ± 2 nm, which is maintained in the pH range of 4.2–10; while the zeta potential is significantly affected, decreasing from 20 ± 2 mV to −5 ± 1 mV at the same pH range. The temperature profiles of PPN suspensions were obtained using a NIR laser beam (1.5 W centered at 808 nm). These results were analyzed with a three-dimensional predictive unsteady-state heat transfer model that considers heat conduction, photothermal heating from laser irradiation, and heat generation due to the water absorption. The temperature profiles of PPN under laser irradiation are concentration-dependent, while the pH increase only induces a slight reduction in the temperature profiles. The model predicts a value of photothermal transduction efficiency ($\eta$) of 0.68 for the PPN. Furthermore, a linear dependency was found for the overall heat transfer coefficient ($U$) and $\eta$ with the suspension temperature and pH, respectively. Finally, the model developed in this work could help identify the exposure time and concentration doses for different tissues and cells (pH-dependent) in photothermal applications.