In the present study, wave propagation characteristics of double-walled boron nitride nanotubes (DWBNNTs) conveying ferrofluid is investigated. Magnetite (Fe3O4) nanofluid is selected as a conveying fluid which reacted in presence of magnetic field. Shear effects of surrounded medium are taken into account using Pasternak model. Stress and strain–inertia gradient elasticity theories are used due to their capability to interpret size effect. Based on Hamilton’s principle and employing Euler–Bernoulli, Timoshenko and Reddy beam models, wave equations of motion in double-walled boron nitride nanotubes are derived and solved by harmonic solution. Regarding the various types of flow regimes in fluid–structure interaction, the upstream and downstream phase velocities of double-walled boron nitride nanotubes conveying ferrofluid are calculated. A detailed parametric study is conducted to clarify the influences of the beam models, size effect theories, magnetic field, surrounding elastic medium and fluid velocity on the wave propagation of double-walled boron nitride nanotubes conveying ferrofluid. The results indicated that in lower wave numbers, the effect of flowing fluid and the difference between the upstream and downstream phase velocities were considerable. The results of this work can be used in design and manufacturing of nanopipes and nanovalves conveying fluid flow to avoid water hammer phenomenon.