Plant aerial parts are differentiated from stem cells that are located in the shoot apical meristem (SAM). CLAVATA3 (CLV3)-CLV1 is a well-known ligand-receptor pair, which functions in SAM maintenance. In Lotus japonicus, HYPERNODULATION ABERRANT ROOT FORMATION1 (HAR1) shows the highest similarity with CLV1 of all Arabidopsis receptor-like kinases (RLKs). However, HAR1 functions in the systemic regulation of root nodule development, but does not appear to function in SAM maintenance. Therefore, the gene that is responsible for SAM maintenance in L. japonicus is largely unknown. Here, we identified the L. japonicus CLV3-like (LjCLV3) gene as a counterpart of AtCLV3 and performed expression and functional analysis. LjCLV3 transcripts were detected in the central region of the shoot meristems. However, unlike AtCLV3, LjCLV3 expression was not detected in the epidermal layer, but in the inner layers of the shoot meristems. RNA interference (RNAi) of LjCLV3 caused enlargement of not only the SAM, but also the primary and secondary inflorescence meristems (IMs). Furthermore, LjCLV3-silenced plants exhibited fasciated stems and an increased number of flowers per peduncle. These results reveal that LjCLV3 is responsible for the maintenance of the SAM as well as the primary and secondary IMs.