Pure silica MFI (Si-MFI) zeolite membranes with desirable hydrophobicity have the potential to separate ethanol/water mixture. However, its separation performance would significantly decrease in the long-term operation due to the presence of silanol groups formed in alkaline media. In this work, silanol-free MFI zeolite membranes were prepared by the incorporation of tungsten in MFI framework. The occurrence of silanol group can be prevented by formation of W–O–Si bridges. The synthesis parameters affected the W-MFI zeolite membranes’ microstructure and separation performance. For 5 wt% ethanol solution, the W-MFI zeolite membranes prepared at optimum condition showed stable separation performance of permeation flux as 2.81 kg m−2 h−1 with separation factor as 32 over 80 h at 60 °C. The membrane was characterized by XRD, DR UV–vis, XPS and 29Si NMR, and the results confirmed the incorporation of W and the absence of silanol groups. This research showed that W-MFI zeolite membranes are promising candidates for ethanol extraction with high stability.