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As the strongest and toughest material known, graphene has found numerous applications in various types of sensors. Due to the great influences of the graphene sheet’s geometry on resonance frequency, circular defects could effect on expected results of sensors. Circular holes in circular graphene sheets (CGSs) have been modeled with molecular dynamics (MD) simulation in the present work. Then the vibration behavior of intact circular plate and circular sheet with the circular defect has been investigated using frequency-domain analysis (FDD). Furthermore, for validating the used method, the obtained natural frequencies for different graphene sheets have been compared with acquired data in former research. The result of validation showed the accuracy of the used method in this study. The results indicated that by increasing the hole size, the natural frequency of a defected sheet with free edges will be diminished, and with simply-supported interior boundary conditions typically went up. Also, by increasing the hole’s eccentricity, the natural frequency of the defected graphene sheet will be diminished when the hole boundary was subjected to simply-support or free condition.