A combination of searches for a new resonance decaying into a Higgs boson pair is presented, using up to 139 fb$^{-1}$ of $pp$ collision data at $\sqrt{s}=13$ TeV recorded with the ATLAS detector at the LHC. The combination includes searches performed in three decay channels: $b\bar{b}b\bar{b}$, $b\bar{b}\tau^+\tau^-$ and $b\bar{b}\gamma\gamma$. No excess above the expected Standard Model background is observed and upper limits are set at the 95% confidence level on the production cross section of Higgs boson pairs originating from the decay of a narrow scalar resonance with mass in the range 251 GeV-5 TeV. The observed (expected) limits are in the range 0.96-600 fb (1.2-390 fb). The limits are interpreted in the Type-I Two-Higgs-Doublet Model and the Minimimal Supersymmetric Standard Model, and constrain parameter space not previously excluded by other searches.