The left–right asymmetry is an essential feature shared by vertebrates. Cilia-driven counterclockwise flow in the mammalian node structure leads to the left–right asymmetric distribution of signals and subsequent asymmetric patterning. Although several signaling pathways have been identified in the specification of node ciliated cells, little is known about the direct downstream effectors of these signaling pathways. Here, we showed that zebrafish Ectoderm-Neural Cortex1-like (enc1l) is expressed in the Kupffer’s Vesicle (KV), an equivalent structure of the mammalian node in zebrafish, and is necessary for KV ciliogenesis. Loss-of-function of enc1l increased the number and decreased the length of KV cilia. The enc1l expression in the KV region was specifically regulated by retinoic acid (RA), FGF, and Wnt signaling pathways. In addition, knocking down enc1l or ectopic enc1l expression was able to rescue the KV cilium defects caused by alteration of RA and FGF signaling, but not Wnt signaling. Taken together, these data indicate thatEnc1l is a direct downstream effector of RA and FGF signaling pathways and modulates KV ciliogenesis in the zebrafish embryo.