Context. XY Ari is the only intermediate polar to show deep X-ray eclipses of its white dwarf. Previously published observations with Ginga and Chandra have also revealed a broad X-ray orbital modulation, roughly antiphased with the eclipse, and presumed to be due to absorption in an extended structure near the edge of an accretion disc. The X-ray pulse profile is generally seen to be double-peaked, although a single-peaked pulse was seen by RXTE during an outburst in 1996. Aims. We intended to investigate the cause of the broad orbital modulation in XY Ari to better understand the accretion flow in this system and other intermediate polars.Methods. We observed XY Ari with RXTE and analysed previously unpublished archival observations of the system made with ASCA and XMM-Newton. These observations comprise six separate visits and span about ten years.Results. The various X-ray observations show that the broad orbital modulation varies in phase and significance, then ultimately disappears entirely in the last few years. In addition, the X-ray pulse profile shows variations in depth and shape, and in the recent RXTE observations displays no evidence for changes in hardness ratio. Conclusions. The observed changes indicates that both the pulse profile and the orbital modulation are solely due to geometrical effects at the time of the RXTE observations, rather than phase-dependent variations in photoelectric absorption as seen previously. We suggest that this is evidence for a precessing, tilted accretion disc in this system. The precession of the disc moves structures out of our line of sight both at its outer edge (changing the orbital modulation) and at its inner edge where the accretion curtains are anchored (changing the pulse profile).