Using observations of X-ray pulsar Her X-1 by the Imaging X-ray Polarimetry Explorer, we report on a highly significant ($>17σ$) detection of the polarization signal from an accreting neutron star. The observed degree of the linear polarization of $∼$10\% is found to be far below theoretical expectations for this object, and stays low throughout the spin cycle of the pulsar. Both the polarization degree and the angle exhibit variability with pulse phase, which allowed us to measure the pulsar spin position angle 57(2) deg and the magnetic obliquity 12(4) deg, which is an essential step towards detailed modelling of the intrinsic emission of X-ray pulsars. Combining our results with the optical polarimetric data, we find that the spin axis of the neutron star and the angular momentum of the binary orbit are misaligned by at least $∼$20 deg, which is a strong argument in support of the models explaining stability of the observed super-orbital variability with the precession of the neutron star.