Abstract The advent of High Temperature Superconductors (HTS) with high field strengths offers the possibility of building smaller, cheaper magnetically confined fusion reactors. However, bombardment by high energy neutrons ejected from the fusion reaction may damage the HTS tapes and impair their operation. Recreating the conditions present in an operational fusion reactor is experimentally challenging, therefore, this work uses molecular dynamics simulations to understand how radiation modifies the underlying crystal structure of YBa2Cu3O7. To facilitate the simulations a new potential was developed that allowed exchange of Cu ions between the two symmetrically distinct sites without modifying the structure. Radiation damage cascades predict the formation of amorphous regions surrounded by regions decorated with Cu and O defects found in the CuO-chains. The simulations suggest that the level of recombination that occurs is relatively low, resulting in a large number of remnant defects and that there is a no substantial temperature effect.