Wheat cell-free expression systems based on wheat germ extract (WGE) enable us to briefly synthesize various types of proteins in vitro merely by exogenously adding their mRNA templates. Moreover, it is possible to produce larger amounts of protein by thoroughly removing the endosperm, which contains many translation inhibitors, including ribonucleases (RNases). However, because small amounts of RNases are also present even in an endosperm-free, high-quality WGE (hqWGE), the in-vitro transcribed mRNA is rapidly degraded. In particular, 3′ exonucleases have been considered as the major RNases that degrade mRNA. We thus herein performed in vitro selection to find an effective, short 3′ protector sequence from a random RNA pool. The selected sequences stabilized in vitro transcripts in the hqWGE more effectively than the previously reported, longer 3′ protectors did. In addition, when one of these 3′ protectors was minimized and then fused to mRNA, the translation efficiency increased 5–6-fold in the hqWGE, mainly due to the mRNA stabilization.