Scrapie is a prion disease characterised by the accumulation of the pathological associated form of cellular prion protein (PrP(SC)) in the central nervous system. Susceptibility to scrapie is associated with polymorphism in the ovine prion protein (PrP) gene. The European Union has implemented scrapie control programs, relying on selective breeding for scrapie resistance; the use of ARR-carrier and the exclusion of VRQ-carrier were recommended. In this study, 4323 individuals from Rasa Aragonesa Sheep breed were genotyped for the PrP gene and the individual estimated breeding values (EBV) for prolificity were calculated. Most represented PrP alleles do not work against prolificity. Only a significant association between VRQ/VRQ genotype and a lower EBV was observed (p = 0.027, eta2 = 0.002). Therefore, avoiding reproduction of VRQ/VRQ individuals would not cause negative effect regarding prolificity.