We present the 78 ks $Chandra$ observations of the $z$ = 6.4 quasar SDSS J1148+5251. The source is clearly detected in the energy range 0.3–7 keV with 42 counts (with a significance ≳9σ). The X-ray spectrum is best fitted by a power law with photon index Γ = 1.9 absorbed by a gas column density of N=2.0$\mathrm{<mrow\; data-mjx-texclass="ORD">-1.5</mrow><mrow\; data-mjx-texclass="ORD">+2.0</mrow>}$ %. We measure an intrinsic luminosity at 2–10 and 10–40 keV equal to ∼ 1.5 × 10$\mathrm{<mrow\; data-mjx-texclass="ORD">45</mrow>}$ erg s$\mathrm{<mrow\; data-mjx-texclass="ORD">-1</mrow>}$, comparable with luminous local and intermediate-redshift quasar properties. Moreover, the X-ray to optical power-law slope value (αOX = −1.76 ± 0.14) of J1148 is consistent with the one found in quasars with similar rest-frame 2500 Å luminosity ($\textit{L}$2500\sim 10$^{32}$\hspace{0.17em}erg\hspace{0.17em}s$^{-1}$\hspace{0.17em}Å$^{-1}$). Then we use $Chandra$ data to test a physically motivated model that computes the intrinsic X-ray flux emitted by a quasar starting from the properties of the powering black hole and assuming that X-ray emission is attenuated by intervening, metal-rich (Z ≥ Z⊙) molecular clouds (MC) distributed on ∼kpc scales in the host galaxy. Our analysis favours a black hole mass MBH ∼ 3 × 10$\mathrm{<mrow\; data-mjx-texclass="ORD">9</mrow>}$ M⊙ and a molecular hydrogen mass M∼2×10$\mathrm{<mrow\; data-mjx-texclass="ORD">10</mrow>}$ M⊙, in good agreement with estimates obtained from previous studies. We finally discuss strengths and limits of our analysis.