A droplet-based electrochemical digital magnetofluidics system has been developed. The system relies on the magnetic movement, in air, of different aqueous microdroplets containing magnetic microparticles—serving as the ‘sample’, ‘blank’, ‘wash’ and ‘reagent’ solutions—into and out of a three-electrode assembly. The movement of all droplets was controlled using the magnetic fields generated by three separate external magnets positioned below the superhydrophobic surface. Square-wave voltammetry was used for rapid measurements of dopamine in multiple successive microdrops with minimal cross talk. The ability of the droplet-based electrochemical microfluidic system to manipulate microliter solutions was also illustrated in bioassays of glucose, involving the merging of enzyme (GOx) and substrate droplets, followed by chronoamperometric measurements of the hydrogen peroxide product in the merged droplet. Variables of the new electrochemical digital magnetomicrofluidic technique were examined and optimized. The new droplet-based electrochemical microfluidic system offers a promising platform for automated clinical diagnostics and drug discovery.