ABSTRACTFollowing the recent COVID‐19 pandemic, mRNA manufacturing processes are being actively developed and optimized to produce the next generation of mRNA vaccines and therapeutics. Herein, the performance of the tangential flow filtration (TFF) was evaluated for high‐recovery, and high‐purity separation of mRNA from unreacted nucleoside triphosphates (NTPs) from the in vitro transcription (IVT) reaction mixture. For the first time, the fouling model was successfully validated with TFF experimental data to describe the adsorption of mRNA on filtration membrane. The fouling model enables monitoring of the mRNA purification processes, designing an appropriate strategy for filter clean‐up, replacing the column at the right time and reducing the process cost. Recovery greater than 70% mRNA without degradation was obtained by implementing a capacity load of ∼19 g/m2, <2.5 psi transmembrane pressure (TMP) and feed flux of 300 LMH. This approach also enables the purification of multiple mRNA drug substance sequences for the treatment of a wide range of different diseases.