The study of the behavior of magnetic skyrmions in local magnetic fields’ nanometric length-scale has gained increasing interest in recent years due to the theoretical proposal of magnetic skyrmion–superconducting vortex pairs as potential hosts for topologically protected bound states, which hold high promise for applications in quantum computing. From a magnetic interaction point-of-view, the key interest lies in understanding the skyrmion dynamics triggered by the magnetic energy landscape generated by the superconducting vortex. Here, we present a micromagnetic study of the dynamics of nanometric skyrmions inside a Gaussian magnetic field profile, which is used as a simplified version of the vortex magnetic flux. On the one hand, our calculations show that local non-linear magnetic fields can be very effective in controlling the dynamics of magnetic skyrmions; in particular, they offer the appealing possibility to manipulate skyrmions in a two dimensional space. On the other hand, they also show that the dynamics of a skyrmion in a local magnetic field can be manipulated via a uniform external magnetic field without any change in the magnetic field gradient. An analytical expression for the skyrmion velocity is given, and the corresponding microscopic dynamics are confirmed by the micromagnetic simulations. This work is expected to motivate more theoretical and experimental studies of the behavior of magnetic skyrmions in proximity to superconducting vortices.