Motivated by results from the LHC and dark matter searches, we study the possibility of phenomenologically viable R-parity violation in $SU(5)$ GUT models from a top-down point of view. We show that in contrast to the more model dependent bounds on the proton lifetime, the limits on neutrino masses provide a robust, stringent and complementary constraint on all $SU(5)$ GUT-based R-parity violating models. Focusing on well-motivated string/$M$ theory GUT frameworks with mechanisms for doublet-triplet splitting and a solution to the $mu/Bmu$ problems, we show that imposing the neutrino mass bounds implies that R-parity violation is disfavored. The arguments can also be generalized to minimal $SO(10)$ GUTs. An experimental observation of R-parity violation would, therefore, disfavor such classes of top-down GUT models.
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