The stability of magnetic skyrmions has been investigated in the past, but mostly in the absence of thermal fluctuations. However, thermal spin fluctuations modify the magnetic properties (exchange stiffness, Dzyaloshinskii-Moriya interaction (DMI) and anisotropy) that define skyrmion stability. Thermal magnons also excite internal skrymion dynamics, deforming the skyrmion shape. Entropy has also been shown to modify skyrmion lifetimes in experiments, but is absent or approximated in previous studies. Here we use metadynamics to calculate the free energy surface of a magnetic thin film in terms of the topological charge and magnetization. We identify the free energy minima corresponding to different spin textures and the lowest energy paths between the ferromagnetic and single skyrmion states. We show that at low temperatures the lowest free energy barrier is a skyrmion collapse process. However, this energy barrier increases with temperature. An alternative path, where a singularity forms on the skrymion edge, has a larger free energy barrier at low temperatures but decreases with increasing temperature and eventually becomes the lowest energy barrier.