Primary cilium is an important hub for cell signaling and dysregulation of primary cilia assembly and disassembly is associated with the development of cancer and chemotherapeutic drug resistance, as well as the genetic disorders collectively known as ciliopathy. β-catenin plays a major role in canonical Wnt signaling; however, its association with primary cilia has only recently been highlighted in reports of β-catenin-mediated primary ciliogenesis. In this study, we found that β-catenin p-S47 was localized to the Golgi apparatus and the nucleus, and the amount of β-catenin p-S47 at these locations was significantly higher during primary ciliogenesis compared with asynchronous cell growth conditions. In addition, the novel β-catenin-binding motor proteins KIF11 and KIFC3 were shown to have a lower binding affinity in β-catenin S47A than in β-catenin wild-type. Knockdown of KIF11 or KIFC3 resulted in primary cilia deficiency and increased β-catenin p-S47 levels in the Golgi apparatus and were accompanied by a decrease in β-catenin p-S47 at the centrosome. The accumulation of β-catenin p-S47 in the nucleus was increased during primary ciliogenesis along with β-catenin-dependent transcriptional activity. The collective findings indicate the existence of a novel mechanism of primary ciliogenesis involving KIF11-/KIFC3-associated β-catenin p-S47 in the Golgi apparatus and β-catenin p-S47 transcriptional activity in the nucleus. This study revealed a new mechanism for the study of ciliopathies, cancer, and chemotherapeutic drug resistance caused by primary ciliogenesis dysregulation and provides new targets for drug development to treat these diseases.