We report the localization of the X-ray emission from two strongly lensed AGN, CLASS B0712+472 (z = 1.34) and CLASS B1608+656 (z = 1.394). We obtain milliarcsecond X-ray astrometry by developing a novel method that combines parametric lens modelling with a Bayesian analysis. We spatially locate the X-ray sources in CLASS B0712+472 and CLASS B1608+656 within 11 mas and 9 mas from the radio source, respectively. For CLASS B0712+472, we find that the X-ray emission is co-spatial with the radio and optical emission. While, in CLASS B1608+656, the X-ray emission is co-spatial with radio, but displaced with respect to the optical emission at 1σ level, which positions this source as an offset AGN candidate. This high astrometric precision improves on the limitations of existing X-ray instruments by two orders of magnitude. The demonstrated method opens a path to search for offset and binary AGN at z > 1, and to directly test supermassive black hole formation models in a redshift range that has been mostly underconstrained to date.