In this work, vibration and stability of fluid-conveying lipid nanotubes are investigated. The first-order shear deformation theory and the nonlocal strain gradient theory are adopted in the model. By using Hamilton’s principle, the governing equations of the present system are obtained. In order to analyze the eigenvalue problem, the modal expansion method is used. Results show that the nonlocal parameter, the length-to-radius ratio, the flow velocity, the material length scale parameter and the solution density have important effect on the free vibration of fluid-conveying lipid nanotubes. Additionally, the current method is validated by comparing with the literature for special cases. The obtained results can be used for the biological application and design of fluid-conveying lipid nanotubes.