Caffeine, as a typical representative of pharmaceutical pollution, was subjected to the removal from water by means of the electro-Fenton process. The study of a single-molecule solution was meant for better understanding of the influence of operating parameters on the removal rates and for finding their optimal values. The setup comprised a bench-scale reactor equipped with a boron-doped diamond anode and a 3D carbon felt cathode. Degradation and mineralization kinetics were monitored for different sets of two major operating parameters: current intensity (from 100 to 1500 mA) and Fe2+ concentration (from 0.1 to 0.5 mM). Experimental data revealed that the optimal catalyst concentration was 0.2 mM, regardless the applied current intensity. For experiments on degradation kinetics, the trend of increasing the reaction rate with an increasing current was valid up to 300 mA. In contrast, the mineralization rate increased up to 1500 mA. The absolute reaction rate constant between caffeine and hydroxyl radical was determined as (2.48 ± 0.01) × 109 M−1 s−1. A follow-up of aromatic compounds, carboxylic acids and inorganic ions, enabled composition of a plausible degradation pathway for caffeine degradation by hydroxyl radicals. An analysis of the operating parameters versus evolution of degradation and mineralization showed that even small concentrations of Fe2+ and low current intensities led to complete degradation and almost complete mineralization.