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Bacterial flagellin has been explored as a potential vaccine adjuvant for enhancing immune responses. In this article, we describe Escherichia coli‐based cell‐free protein synthesis (CFPS) as a method to rapidly produce soluble phase 1 flagellin (FliC) protein from Salmonella typhimurium. The yield was about 300 µg/mL and the product had much higher affinity for the TLR5 receptor (EC50 = 2.4 ± 1.4 pM) than previously reported. The flagellin coding sequence was first optimized for cell‐free expression. We then found that the D0 domain at the C‐terminus of flagellin was susceptible to proteolytic degradation in the CFPS system. Proteolysis was reduced by protease inhibitors, the use of protease‐deficient cell extracts or deletion of the flagellin D0 domain. A human Toll‐Like Receptor 5 (hTLR5)‐specific bioactivity analysis of purified flagellin demonstrated that, although the D0 domain is far from the TLR5 …