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Micro and nanotubes have found major application in fluidic systems as channels for conveying fluid. In some micro and nanofluidic applications such as drug delivery, a transverse magnetic field can be used to guide the fluid flow by generating an axial force in the flow direction. An important issue in the design of micro and nanofluidic systems is the structural vibration caused by the fluid flow. In the current study, we investigate the effect of transverse magnetic field on the vibration of cantilever micro and nanotubes conveying fluid by considering the small size effects. We couple the nonlocal Euler–Bernoulli beam model with Navier–Stokes theory to determine a fluid structure interaction (FSI) model for the vibration analysis of the system. We modify the FSI governing equation by driving a velocity correction factor to consider the effect of transverse magnetic field on the fluid flow's pattern through the tube. Then, we use the Galerkin's method to obtain the frequency diagrams for the instability analysis of the system. We show that the transverse magnetic field can have a substantial effect on the dynamics of tube conveying fluid by increasing the system's natural frequencies and critical flow velocity which contributes to the flutter instability. We also discover that although the transverse magnetic field plays a crucial role on dynamics of microstructures, its effect on the dynamics of nanotubes is not significant and can be ignored. [ABSTRACT FROM AUTHOR]