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Magnetic skyrmions are nano-scale magnetic states that could be used in various spintronics devices. A central issue is the mechanism and rate of various possible annihilation processes and the lifetime of metastable skyrmions. While most studies have focused on classical over-the-barrier mechanism for annihilation, it is also possible that quantum mechanical tunneling through the energy barrier takes place. Calculations of the lifetime of magnetic skyrmions in a two-dimensional lattice are presented and the rate of tunneling compared with the classical annihilation rate. A remarkably strong variation in the onset temperature for tunneling and the lifetime of the skyrmion is found as a function of the values of parameters in the extended Heisenberg Hamiltonian, i.e. the out-of-plane anisotropy, Dzyaloshinskii–Moriya interaction and applied magnetic field. Materials parameters and conditions are identified where the onset of tunneling could be observed on a laboratory time scale. In particular, it is predicted that skyrmion tunneling could be observed in the PdFe/Ir(111) system when an external magnetic field on the order of 6T is applied.