The three‐dimensional long‐wave linear stability of a straight vortex, that runs down a circular tube, parallel with its axis but slightly displaced from it, is analyzed. The vortex flow is modeled by an infinite concentrated, potential vortex filament. The filament is immersed in an axial uniform flow, and autorotates around the tube axis due to its small eccentricity. The tube walls are modeled by a surface distribution of potential sources. Results show that the vortex develops a dynamic instability in a narrow range of wave numbers as a direct result of its small eccentricity. The vortex also tends to diverge statically at certain wave numbers, only when it is in a ‘‘subcritical’’ state. Finally, it is shown that a time‐dependent streamwise variation of the tube radius can be used as a controller to actively control the dynamic stability of an eccentric vortex in a tube.