The growth in speed and density of programmable logic devices, such as Field programmable gate arrays (FPGA), enables sophisticated designs to be created within a short time frame. The flexibility of a programmable device alleviates the difficulty of the integration of a design with a wide range of components on a single chip. FPGAs bring both performance and power efficiency, especially for compute or data-intensive applications. Efficient and accurate mRNA quantification is an essential step for molecular signature identification, disease outcome prediction, and drug development, which is a typical compute- and data-intensive compute workload. In this work, I propose to accelerate mRNA quantification with FPGA implementation. I analyze the performance of mRNA Quantification with FPGA, which shows better or similar performance compared to that of CPU implementation.