The presence of pharmaceutical products in the water cycle may cause harmful effects such as morphological, metabolic and sex alterations in aquatic organisms and the selection/development of organisms resistant to antimicrobial agents. The compounds’ stability and persistent character hinder their elimination by conventional physico-chemical and biological treatments and thus, the development of new water purification technologies has drawn great attention from academic and industrial researchers. Recently, the electro-Fenton process has been demonstrated to be a viable alternative for the removal of these hazardous, recalcitrant compounds. This process occurs under the action of a suitable catalyst, with the majority of current scientific research focused on heterogeneous systems. A significant area of research centres working on the development of an appropriate catalyst able to overcome the operating limitations associated with the homogeneous process is concerned with the short service life and difficulty in the separation/recovery of the catalyst from polluted water. This review highlights a present trend in the use of different materials as electro-Fenton catalysts for pharmaceutical compound removal from aquatic environments. The main challenges facing these technologies revolve around the enhancement of performance, stability for long-term use, life-cycle analysis considerations and cost-effectiveness. Although treatment efficiency has improved significantly, ongoing research efforts need to deliver economic viability at a larger scale due to the high operating costs, primarily related to energy consumption.