The Scibar Cosmic-Ray Telescope (SciCRT) is a brand new detector of the Sierra Negra Cosmic Rays Observatory (SN-CRO). It is designed to observe solar neutrons and the muon background produced by galactic cosmic rays. In this work we present a Geant4-based simulation of the muon detection efficiency of the SciCRT; for this purpose we injected 10$^{5}$ muons, in an energy range from 100 to 1000 MeV, impinging the SciCRT array. Our results provide new information about the SciCRT performance and may be used to study variations in low energy galactic cosmic rays.