Metallo‐base pairs have been extensively studied for applications in nucleic acid‐based nanodevices and genetic code expansion. Metallo‐base pairs composed of natural nucleobases are attractive because nanodevices containing natural metallo‐base pairs can be easily prepared from commercially available sources. Previously, we have reported a crystal structure of a DNA duplex containing THgIIT base pairs. Herein, we have determined a high‐resolution crystal structure of the second natural metallo‐base pair between pyrimidine bases CAgIC formed in an RNA duplex. One AgI occupies the center between two cytosines and forms a CAgIC base pair through N3AgIN3 linear coordination. The CAgIC base pair formation does not disturb the standard A‐form conformation of RNA. Since the CAgIC base pair is structurally similar to the canonical Watson–Crick base pairs, it can be a useful building block for structure‐based design and fabrication of nucleic acid‐based nanodevices.