Abstract 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 ${\rm N}_{\rm H}=2.0^{+2.0}_{-1.5}\times {10}^{23}\,{\rm cm}^{-2}$ . We measure an intrinsic luminosity at 2–10 and 10–40 keV equal to ∼ 1.5 × 1045 erg s− 1, 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 (L 2500 ∼ 1032 erg s − 1 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 M BH ∼ 3 × 109 M⊙ and a molecular hydrogen mass $M_{\rm H_2}\sim 2\times {10}^{10}\ {\rm M_{\odot }}$ , in good agreement with estimates obtained from previous studies. We finally discuss strengths and limits of our analysis.