The use of the pulsed current can be an alternative to decrease the electrode polarization, as well as achieving lower energy consumption. This study investigated the electrocoagulation through pulsed current for the removal of natural organic matter from water. The experiments were carried out using Box–Behnken factorial design with the response surface methodology for the design of experiments, modeling and interpreting of the results. The electrocoagulation cell consisted of an acrylic reactor with 4 L capacity with four electrodes of aluminum, in parallel connection mode. The experimental independent variables studied were: current density (5.5 to 44.5 A m−2), electrodes spacing (2 to 7.6 mm), stirring rate (200 to 1,000 rpm), frequency (500 to 5,000 Hz), humic acid concentration (5 to 20 mg L−1) and NaCl (100 to 300 mg L−1) as supporting electrolyte, evaluating the residual apparent color (RAC) and electric energy consumption (EEC). The pH of the solution increased during the experiments, reaching basic values. The response surface regression procedure was employed to fit the second-order polynomial, and the model fitted well to the obtained values, reaching R2 0.9995 (RAC) and R2 0.9989 (EEC). The lowest RAC was 11.8 Hazen units (96.2% color removal), where the EEC was 0.393 kWh m−3.