The dynamic interaction between positive and negative signals is necessary for remodeling of postsynaptic structures at the neuromuscular junction (NMJ). Here we report that Wnt3A negatively regulates acetylcholine receptor (AChR) clustering by repressing the expression of Rapsyn, an AChR-associated protein essential for AChR clustering. In cultured myotubes, treatment with Wnt3A or over- expression of β-catenin, the condition mimicking the activation of Wnt canonical pathway, inhibited Agrin-induced formation of AChR clusters. Moreover, Wnt3A treatment promoted dispersion of AChR clusters, and this effect was prevented by DKK1, an antagonist of the Wnt canonical pathway. Next, we investigated possible mechanisms underlying Wnt3A regulation of AChR clustering in cultured muscle cells. Interestingly, we found that Wnt3A treatment caused a decrease in the protein level of Rapsyn. In addition, Rapsyn promoter activity in cultured muscle cells was inhibited by the treatment with Wnt3A or β-catenin over-expression, which probably inhibits the action of transcription factor P65. Forced-expression of Rapsyn driven by a promoter that is not responsive to Wnt3A prevented the dispersing effect of Wnt3A on AChR clusters, suggesting that Wnt3A indeed acts to disperse AChR clusters by down-regulating the expression of Rapsyn. The role of Wnt/β-catenin signaling in dispersing AChR clusters was also investigated in vivo by electroporation of Wnt3A or β-catenin into mouse limb muscles, where ectopic Wnt3A or β-catenin caused disassembly of postsynaptic apparatus. Together, these results suggest that Wnt/β-catenin signaling plays a negative role for postsynaptic differentiation at the NMJ, probably by regulating the expression of synaptic proteins, such as Rapsyn.