A search for flavour-changing neutral current (FCNC) $tqH$ interactions involving a top quark, another up-type quark ($q=u$, $c$), and a Standard Model (SM) Higgs boson decaying into a $\tau$-lepton pair ($H\rightarrow \tau^+\tau^-$) is presented. The search is based on a dataset of $pp$ collisions at $\sqrt{s}=13$ TeV that corresponds to an integrated luminosity of 139 fb$^{-1}$ recorded with the ATLAS detector at the Large Hadron Collider. Two processes are considered: single top quark FCNC production in association with a Higgs boson ($pp\rightarrow tH$), and top quark pair production in which one of top quarks decays into $Wb$ and the other decays into $qH$ through the FCNC interactions. The search selects events with two hadronically decaying $\tau$-lepton candidates ($\tau_{\text{had}}$) or at least one $\tau_{\text{had}}$ with an additional lepton ($e$, $\mu$), as well as multiple jets. Event kinematics are used to separate signal from the background through a multivariate discriminant. A slight excess of data is observed with a significance of 2.3$\sigma$ above the expected SM background, and 95% CL upper limits on the $t\to qH$ branching ratios are derived. Observed (expected) 95% CL upper limits are set on the $t\to cH$ and $t\to uH$ branching ratios of $9.4 \times 10^{-4}$ $(4.8^{+2.2}_{-1.4}\times 10^{-4})$ and $6.9\times 10^{-4}$ $(3.5^{+1.5}_{-1.0}\times 10^{-4})$, respectively. The corresponding combined observed (expected) upper limits on the dimension-6 operator Wilson coefficients in the effective $tqH$ couplings are $C_{c\phi} <1.35$ $(0.97)$ and $C_{u\phi} <1.16$ $(0.82)$, respectively.

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