The LHC is a top factory and Run 2 has delivered billions of top quarks to the experiments. In this contribution, the results are presented of searches by the ATLAS experiment for Charge Lepton Flavour Violation, and rare flavour-changing neutral current interactions of the top quark. Flavour changing neutral currents (FCNC) analyses combine search criterion targeted at top quark decays $t\rightarrow qX$ with regions aimed at single top quark production $pp\rightarrow tX$, where $X$ is either a gluon, photon, \textit{Z}-boson or a Higgs boson. The large data set, together with advanced analysis techniques, allow to improve the sensitivity very significantly and competitive bounds on the equivalent branching fraction $\mathcal{B}(t\rightarrow qH)$ are presented.