Abstract We report X-ray observations of the most distant known gravitationally lensed quasar, J0439+1634 at z = 6.52, which is also a broad absorption line (BAL) quasar, using the XMM-Newton Observatory. With a 130 ks exposure, the quasar is significantly detected as a point source at the optical position with a total of 358 − 19 + 19 net counts using the EPIC instrument. By fitting a power law plus Galactic absorption model to the observed spectra, we obtain a spectral slope of Γ = 1.45 − 0.09 + 0.10 . The derived optical-to-X-ray spectral slope α ox is − 2.07 − 0.01 + 0.01 , suggesting that the X-ray emission of J0439+1634 is weaker by a factor of 18 than the expectation based on its 2500 Å luminosity and the average α ox versus luminosity relationship. This is the first time that an X-ray weak BAL quasar at z > 6 has been observed spectroscopically. Its X-ray weakness is consistent with the properties of BAL quasars at lower redshift. By fitting a model including an intrinsic absorption component, we obtain intrinsic column densities of N H = 2.8 − 0.6 + 0.7 × 10 23 cm − 2 and N H = 4.3 − 1.5 + 1.8 × 10 23 cm − 2 , assuming a fixed Γ of 1.9 and a free Γ, respectively. The intrinsic rest-frame 2–10 keV luminosity is derived as (9.4–15.1) × 1043 erg s−1, after correcting for lensing magnification (μ = 51.3). The absorbed power-law model fitting indicates that J0439+1634 is the highest redshift obscured quasar with a direct measurement of the absorbing column density. The intrinsic high column density absorption can reduce the X-ray luminosity by a factor of 3–7, which also indicates that this quasar could be a candidate intrinsically X-ray weak quasar.