Conventional irreversible electroporation (IRE) and high-frequency irreversible electroporation (H-FIRE) pulses have been widely employed in many biomedical and food applications. To investigate the effect of Joule heating generated by pulsed electric fields on cell electroporation, single-cell electroporation models without (EP only) and with the consideration of Joule heating (EP+T) were subjected to the equivalent energy IRE and H-FIRE pulses. The simulation results showed that with the consideration of Joule heating, the transmembrane voltage of the anodic point (TMPA) reached the electroporation threshold (∼1 V) faster, and a significant increase in the plasma membrane conductivity (σA) and pore number (kp) was found. We further evaluated the effect of the pulse burst repetition frequency (PBRF) of H-FIRE pulses on cell electroporation based on the EP+T model, and discovered kp increased with frequency when PBRF lower than 2 kHz, whereas it decreased with frequency for PBRF higher than 2 kHz. The accumulation of the ratio of the perforation area to the cell membrane area (sum of Ap/A) during the 400th pulse was also reversed when PBRF was 2 kHz. Our results indicated that Joule heating generated by repetitive pulse delivery would facilitate electroporation, and the effect of PBRF on cell electroporation was non-monotonic.