The associated production of the Higgs boson with a pair of top/anti-top quarks ($t\bar t H$) is the only process providing the direct access to the measurement of the Yukawa coupling between the Higgs boson and the top quark. The presented results exploit the data collected during 2015 and 2016 by the ATLAS experiment during LHC collisions at a center-of-mass energy of 13 TeV. Multivariate analysis techniques are used in order to discriminate the signal from the very large backgrounds arising mainly from top-quark pair production. In addition, for the first time the analysis uses algorithms specifically designed to cope with the challenging reconstruction of hadronically decaying high-$p_\mathrm{T}$ bosons and top quarks. The combined best fit value of the signal strength is found to be $0.84^{+0.64}_{-0.61}$, while a value greater than $2.0$ is excluded at 95\% confidence level while the expected upper limit is $\mu < 1.2$ in the absence of a $t\bar t H$ signal.