The Chočské vrchy Mts. are a part of the Tatra–Fatra Belt located in the Central Western Carpathians (Slovakia). We characterize the main Late Cretaceous–Cenozoic deformation events and the changing strain that formed the geological setting of the Chočské vrchy Mts. by applying the Anisotropy of Magnetic Susceptibility coupled with the Anisotropy of Anhysteretic Remanent Magnetization and complemented by petromagnetic analyses. We analyse Lower Cretaceous marly limestones of the Mraznica Formation (Fm.), which is a part of the Krížna nappe, and the “post-thrusting” Eocene–Oligocene Huty Fm. Petromagnetic experiments reveal that paramagnetic minerals control the magnetic susceptibility, although a distinct contribution of ferromagnetics (magnetite, hematite and likely pyrrhotite) is also documented. The magnetic fabric in both the Mraznica and Huty fms. is generally sedimentary with minor tectonic imprint. The NNE–SSW orientation of the magnetic lineation in most of the Mraznica Fm. sites corresponds well with the local bedding strike as well as the calculated regional statistical fold axis for the Krížna nappe, but it deflects from the expected orientation considering the regional Cretaceous thrusting direction. Similarly oriented magnetic lineation is also documented in some Huty Fm. sites. Magnetic and structural results reveal the dip of the post-trusting Paleogene strata covering the Chočské vrchy Mts. horst block differs from both the dip of magnetic lineation and the dip of statistical fold axis from the Krížna nappe within this uplifted block, suggesting complex uplift-related deformations. We conclude that Krížna nappe folds together with AMS lineation, both formed during Late Cretaceous thrusting, have been later rotated by an angle of 20° as an effect of Neogene transpression, which also affected the magnetic fabric of the post-thrusting cover.