Enol ether structural motifs exist in many highly oxygenated biologically active natural products and pharmaceuticals. The synthesis of the geometrically less stable Z-enol ethers is challenging. An efficient Z-selective oxidative isomerization process of allyl ethers catalyzed by a cobalt(II) (salen) complex using N-fluoro-2,4,6-trimethylpyridinium trifluoromethanesulfonate (Me3NFPY•OTf) as an oxidant has been developed. Thermodynamically less stable Z-enol ethers were prepared in excellent yields with high geometric control. This methodology also demonstrates the effectiveness in controlling the Z-selective isomerization reaction of diallyl ethers at room temperature. This catalytic system provides an alternative pathway to extend the traditional reductive isomerization of allyl ethers.