The gene encoding a thermostable l-aminoacylase (LAA) from Deinococcus radiodurans BCRC12827 was isolated and expressed in transgenic rice under the control of a rice actin gene promoter or a seed-specific promoter, Ose705. The recombinant LAA in the transgenic line Ose705:LAA was specifically detected in rice grains, but not in leaves, and its identity was confirmed by a LC/MS/MS assay. Furthermore, was efficiently purified via affinity chromatography using a nickel column. Enzymatic activity of this rice-produced LAA was determined by HPLC and a maximum activity at pH 8.0 and 45 °C in a phosphate buffer supplemented with the divalent metal ion Co2+ using NAc-l-HPA as a substrate was obtained, similar to its host counterpart. This rice-produced LAA maintained approximately 50% enzyme activity after 48 h of incubation under 45 °C and maintained approximately 90% activity compared to a freshly prepared sample after being stored in rice seeds for 4 years. The present study indicated that seed-specific protein production in transgenic rice is a good and safe source for mass production of LAA, and this system can be useful for the production of other biomedical proteins as well.