Ion channels play critical roles in the physiology and function of the nervous system and contractile tissue; however, their role in non-contractile tissue and embryonic development is less understood. Tracheobronchomalacia (TBM) and complete tracheal rings (CTR) are disorders affecting the muscle and cartilage of the trachea and bronchi, whose etiology remains poorly understood. We demonstrated that trachealis muscle organization and polarity are disrupted after the deletion of Wls, an essential component of the Wnt signaling pathway, in the tracheal epithelium during embryonic development. The changes are similar to the anomalous trachealis muscle observed after the deletion of ion channel genes in developing mouse trachea. We hypothesize that Wnt signaling influences the expression of ion channels to promote trachealis muscle cell assembly and patterning. Deleting Wls in developing trachea causes differential regulation of genes mediating actin binding, cytoskeleton organization, and potassium ion channel activity. Wnt/β-catenin dependent signaling regulated expression of Kcnj13, Kcnd3, Kcnj8, and its related receptor, Abcc9, as demonstrated by in vitro studies and in vivo analysis in Wnt5a and β-catenin deficient tracheas. Pharmacological inhibition of potassium ion channels and Wnt signaling impaired contractility of developing trachealis smooth muscle and formation of cartilaginous mesenchymal condensation. Thus, epithelial-induced Wnt/β-catenin signaling mediates trachealis muscle and cartilage development via modulation of ion channel expression to promote trachealis muscle architecture, contractility, and cartilaginous extracellular matrix in mouse trachea. Ion channel activity may influence tracheal morphogenesis underlying TBM and CTR.