The implementation of pulse current in an electro-Fenton process was explored for the removal of humic acid (HA). The impacts of different operating variables, including initial HA concentration (C0 = 10–50 mg/L), initial pH (pH0 = 3–10), electrical conductivity (EC0 = 500–3000 μS/cm), pulse time (Tpls = 20–200 min), voltage (V = 5–30 volts), and reaction time (t = 10–60 min) on the removal efficiency of HA were explored. The response surface methodology (RSM) was implemented to decrease the number of experiments, and to evaluate the impacts of the model components and the optimal conditions of the process. The maximum removal efficiency (97.2%) with the lowest electrical energy usage (1.02 kWh/kg HA removal) was obtained with the operating conditions of initial HA concentration 50 mg/L, initial pH 3, electrical conductivity 500 μS/cm, pulse time 20 min, voltage 5 V, and reaction time 60 min. For the best HA removal efficiency, the optimum operating conditions of the model components were determined as initial HA concentration 20 mg/L, initial pH 6, electrical conductivity 526 μS/cm, pulse time 200 min, voltage 5 V, and reaction time 10 min. For HA removal efficiency, the determination coefficient (R2) of 0.885 and its estimated value of 0.7985 were in line with the adjusted R2 of 0.8532. This study clarified the considerable effects of such studied process-related parameters as pH, HA concentration, applied voltage, and pulse time, and the findings also revealed that the electro-Fenton process to be a powerful and encouraging application for HA removal.