Intracellular delivery of messenger RNA (mRNA) is a promising approach for experimental and therapeutic manipulation of cellular activity. However, environmental RNase hinders reliable handling of mRNA for experimental and therapeutic use. In this study, biodegradable capsules composed of dextran sulfate and poly-l-arginine in the layer-by-layer (LbL) fashion are employed for the protection and delivery of mRNA. Our results demonstrate that addition of RNase inhibitors to mRNA while co-precipitation with CaCO3 and subsequent LbL encapsulation are both crucial to preserve the integrity of mRNA. The expression of functional luciferase enzyme in HEK293T human embryonic kidney cells after incubation with synthetic luciferase-encoding mRNA capsules indicates the reliability of the encapsulating system and cellular intake of functional mRNAs. These improvements in mRNA encapsulation should provide essential basis for microcapsule-based mRNA delivery for further applications.