Fluid shear stress (FSS) may alter ciliary structures and ciliogenesis, and it has been reported that the Wnt signaling pathway may regulate cilia assembly and disassembly. The present study aimed to investigate the effects of FSS on primary cilia, the Wnt/β‑catenin and Wnt/PCP signaling pathways, and the association among them. In the present study, human umbilical vein endothelial cells were subjected to FSS of differing velocities for various periods of time using a shear stress device. Subsequently, immunofluorescence and quantitative polymerase chain reaction were used to detect the expression and localization of the following core proteins: β‑catenin in the Wnt/β‑catenin signaling pathway; and dishevelled segment polarity protein 2 (Dvl2), fuzzy planar cell polarity protein (Fuz) and VANGL planar cell polarity protein 2 (Vangl2) in the Wnt/planar cell polarity (PCP) signaling pathway. Furthermore, the colocalization of Dvl2 with the basal body was analyzed under low FSS and laminar FSS. The results demonstrated that low FSS promoted the expression of Dvl2 and its colocalization with the basal body. Although Fuz expression was decreased with increasing duration of FSS, no visible alterations were detected in its localization, it was ubiquitously localized in the ciliated region. Conversely, the expression of Vangl2 was increased by laminar FSS, and β‑catenin was translocated into the nucleus at the early stage of low FSS. These findings suggested that Dvl2 may participate in low FSS‑induced ciliogenesis and β‑catenin may participate at the early stage, whereas Vangl2 may be associated with laminar FSS‑induced cilia disassembly.