Magnetic skyrmions are prime candidates for future information technology, and their fate in devices is settled by the defects they encounter. In ultrathin films, skyrmions can be as small as a couple of nanometers, carrying only a few tens of magnetic moments, while atomic defects reshape their energy landscape on the atomic scale. Here, we demonstrate that such ultrasmall skyrmions can behave quantum mechanically and that their quantum dynamics is unusual. Since the gyrotropic force dominates, the two coordinates of a ferromagnetic skyrmion are canonically conjugate and the skyrmion behaves as a particle in the lowest Landau level of an effective magnetic field, with a magnetic length of 0.6 Å. Utilizing skyrmion-defect interaction profiles of Cr and Fe adatoms and dimers in PdFe/Ir(111), obtained from atomistic spin simulations parametrized from first principles, we unveil quantized gyrotropic orbits with level spacings of 20–85~μeV, bound not only by pinning defects but also, counter-intuitively, by repulsive ones. Saddle points of the energy landscape act as quantum beam splitters for skyrmions, and quantum depinning reaches rates of 1–100 Hz below the critical current. Embedded impurities, in contrast, bind the skyrmion so strongly that it ceases to behave as a rigid particle, defining a strong-coupling regime. For the Gilbert damping typical of ultrathin films, the quantized levels remain well resolved. The thermal-to-quantum crossover lies between 40 and 160 mK, which is within reach of millikelvin scanning tunneling microscopy, where tip-induced escape statistics and electron spin resonance STM can reveal the quantized gyrotropic motion of skyrmions pinned at defects crafted atom by atom.