In contrast, high-throughput experimentation has transformed the pharmaceutical sector, yet to our knowledge, no high-throughput methods currently exist for assessing anion transport activity. Such methodologies hold great promise for alleviating the experimental bottlenecks associated with traditional assays, enhancing time efficiency, and enabling the evaluation of more extensive compound libraries, which can lead to quicker hit identification and more comprehensive structure-activity relationship studies. There is an increasing trend towards the integration of automated workflows as cost-effective and productivity-enhancing strategies within medicinal chemistry, fuelled by advancements in automated synthesis, purification, and biological assessment. In this work, we present the design of high-throughput anion antiport assays that significantly enhance the throughput of ion transport workflows. We have adapted the established lucigenin assay into high-throughput formats utilising commonly accessible fluorescence plate reader technology. Initially, we developed a manual preparation method for a 96-well plate format using multi-channel pipettes, followed by creating semi-automated and automated workflows for 384-well plates employing the Opentrons OT-2 liquid handling platform. Our assays have been benchmarked against literature compounds previously evaluated via ion-selective electrode assays, demonstrating a strong correlation (R² = 0.99 -0.89). This publication aims to provide detailed methodologies and the necessary files for plate-reader setup and data analysis, thereby making these methods accessible to other researchers. We anticipate that these techniques will facilitate the rapid evaluation of extensive compound libraries, enabling future studies to explore a wider chemical space and align more closely with the methodologies favoured by the pharmaceutical industry.