A search for resonant and non-resonant pair production of Higgs bosons in the $b\bar{b}\tau^+\tau^-$ final state is presented. The search uses 36.1 fb$^{-1}$ of $pp$ collision data with $\sqrt{s}= 13$ TeV recorded by the ATLAS experiment at the LHC in 2015 and 2016. The semileptonic and fully hadronic decays of the $\tau$-lepton pair are considered. No significant excess above the expected background is observed in the data. The cross-section times branching ratio for non-resonant Higgs boson pair production is constrained to be less than 30.9 fb, 12.7 times the Standard Model expectation, at 95% confidence level. The data are also analyzed to probe resonant Higgs boson pair production, constraining a model with an extended Higgs sector based on two doublets and a Randall-Sundrum bulk graviton model. Upper limits are placed on the resonant Higgs boson pair production cross-section times branching ratio, excluding resonances $X$ in the mass range 305~{\rm GeV} < m_X < 402~{\rm GeV} in the simplified hMSSM minimal supersymmetric model for $\tan\beta=2$ and excluding bulk Randall-Sundrum gravitons $G_{\mathrm{KK}}$ in the mass range 325~{\rm GeV} < m_{G_{\mathrm{KK}}} < 885~{\rm GeV} for $k/\overline{M}_{\mathrm{Pl}} = 1$.

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