Abstract: Photoelectrochemical detection of nucleic acid-based cancer biomarkers offers opportunities for highly sensitive, selective, and fast quantitative detection using low-cost measurement instruments. In order to establish itself as a standard method for identifying and quantifying nucleic acids, we have developed a multiplexing strategy using LED technology for photoelectrochemical detection in 96 samples simultaneously. A dedicated setup based on the 96-well plate configuration with a custom-made 96-well LED array was developed. Subsequently, a proof-of-concept study was performed for three miRNAs that are associated with prostate cancer, i.e., miRNA-141, miRNA-145, and miRNA-375. First, measurements with photosensitizer chlorin e6 and redox reporter hydroquinone free in solution proved the proper functioning of the multiplexed detection. Second, the photoelectrochemical detection of the three miRNAs at 24 nM levels was successfully demonstrated. Thereafter, linear calibration curves (R2 > 0.9 for all analytes) were made with plasma spiked with 8–500 pM miRNA. This work presents the first system for multiplexed high-throughput photoelectrochemical detection, allowing it potentially to become a cost-effective and faster alternative to RT-qPCR and gene sequencing techniques in the future.