Stellar prolate rotation in dwarf galaxies is rather uncommon, with only two known galaxies in the Local Group showing such feature (Phoenix and And II). Cosmological simulations show that in massive early-type galaxies prolate rotation likely arises from major mergers. However, the origin of such kinematics in the dwarf galaxies regime has only been explored using idealized simulations. Here, we made use of hydrodynamical cosmological simulations of dwarfs galaxies with stellar mass between 3 × 105 and 5 × 108 M⊙ to explore the formation of prolate rotators. Out of 27 dwarfs, only one system showed clear rotation around the major axis, whose culprit is a major merger at $z$ = 1.64, which caused the transition from an oblate to a prolate configuration. Interestingly, this galaxy displays a steep metallicity gradient, reminiscent of the one measured in Phoenix and And II: this is the outcome of the merger event that dynamically heats old, metal-poor stars, and of the centrally concentrated residual star formation. Major mergers in dwarf galaxies offer a viable explanation for the formation of such peculiar systems, characterized by steep metallicity gradients and prolate rotation.