This Letter presents direct searches for lepton flavour violation in Higgs boson decays, $H\rightarrow e\tau$ and $H\rightarrow\mu\tau$, performed with the ATLAS detector at the LHC. The searches are based on a data sample of proton-proton collisions at a centre-of-mass energy $\sqrt{s} = 13$ TeV, corresponding to an integrated luminosity of $36.1\,\mathrm{fb}^{-1}$. No significant excess is observed above the expected background from Standard Model processes. The observed (median expected) 95 % confidence-level upper limits on the lepton-flavour-violating branching ratios are $0.47\%$ ($0.34^{+0.13}_{-0.10}\,\%$) and $0.28\%$ ($0.37^{+0.14}_{-0.10}\,\%$) for $H\to e\tau$ and $H\to\mu\tau$, respectively.