Cell monolayers, including endothelial cells lining the vasculature and blood-brain barrier, and epithelial cells lining the lung airways and gut, form a semipermeable barrier across which transport of biomolecules is tightly regulated. The assessment of barrier function is therefore critical in in vitro models of barrier-forming tissues, including microfluidic organ-on-a-chip models. Cell monolayer barrier function is commonly assessed using a fluorescent tracer-based permeability assay in both conventional Transwell and organ-on-a-chip models, but this method requires laborious manual sampling, bulky instrumentation and offline sample processing. In this work, we introduce a novel on-chip microfluidic permeability assay that replaces the traditional fluorescent tracer with an electroactive tracer. Similar to methods such as TEER, the electrochemical permeability assay eliminates the need for manual sampling and complex optical instrumentation. We validated the method by demonstrating close agreement between experimental and numerically-simulated diffusive and convective transport in the microfluidic device. Different electroactive tracers were screened for efficient electron transfer, stability and inertness relative to the cell monolayer. The assay was then used to measure the permeability of endothelial cells cultured under both static and flow culture conditions, and after exposure to a permeability mediator. In summary, the electrochemical permeability assay combines the simplicity of tracer-based permeability methods with the benefits of on-chip integration, which will ultimately facilitate the robust multiparametric characterization of barrier function in microfluidic organs-on-chips.