The Morgado Superior Rock Shelter is located near the city of Tomar, in Central Portugal. This site presents important funerary contexts that according to published information encompass the Neolithic, Chalcolithic and Bronze Age. Other non-funerary uses have not yet been characterised but were briefly suggested. A faunal sample of the 1988 and 2012 interventions is analysed from a zooarchaeological and taphonomical perspective, focusing on the leporid remains that largely dominate the assemblage. Clear indicators of a human origin are absent, while a configurational approach allows the description of exogenous and intrusive origins. The characteristics of the registered consumption taphonomical indicators are suggestive of scat and non-ingested accumulation by foxes. Furthermore, this study allows us to discuss some aspects of the formation of the stratigraphy of this important cave necropolis, while also serving as an example of the expected results of foxes' action on leporid remains in an archaeological site.