Pharmaceuticals have low biodegradability and can retain their chemical structure for long periods of time leading to an accumulation in the environment causing irreversible changes. Electrochemical oxidation has been proved to be an environmentally friendly and economically viable solution for bio-refractory of organic molecules as well as for the disinfection of wastewaters. This paper aims to evaluate the performance of specific energy consumption for a given reduction of toxic organic compound loads in a continuous flow bipolar packed-bed electrochemical reactor and compare this with a classical parallel plate reactor. The energy cost for both the parallel plate and bipolar electrochemical reactors are similar (around 1.6 kWh m-3) lower than other advanced oxidation process reported in literature. However, the bipolar configuration is particularly suitable for low conductivity waste water and/or for avoiding the formation of organochloride compounds in a chloride rich wastewater.