Processing-in-memory (PIM) architecture has been considered as a promising solution for the “memory-wall” issue in many data-intensive applications, especially in bioinformatics. Recent works of developing PIM for genome alignment and assembling have achieved tremendous improvement, while another important genome analysis - mRNA quantification has not been explored. Efficient and accurate mRNA quantification is a crucial step for molecular signature identification, disease outcome prediction and drug development. In this paper, for the first time, we propose a SOT-MRAM based PIM platform, named PIM-Quantifier, for efficient mRNA quantification. A PIM-friendly alignment-free quantification algorithm is first proposed. Then, we present the optimized PIM architecture/circuit designs and mapping method to efficiently accelerate mRNA quantification. Extensive experiments show that PIM-Quantifier significantly improves mRNA quantification performance than CPU and recent other PIM platforms in efficiency defined as throughput/power.