The behaviour of semiconducting graphene quantum dots (GQDs), as good candidates for various biological carrier applications and optical sensing, are necessary to be studied under various conditions. In this study, GQD models were generated according to the geometrical and chemical specifications of synthesized GQDs to achieve the most realistic models. The GQDs’ bandgap and distribution of their electric surface charges were obtained using computational chemistry method. Finite element analysis was conducted on pristine and defective GQDs to study Young and shear modulus. Buckling load and resonant frequency modes of GQDs were calculated analytically and demonstrated under various boundary conditions. The dimension of GQDs has an average of 3.5 ± 0.4 nm, with an interlayer spacing of 0.36–0.40 nm. Computational chemistry studies revealed the characteristic zero-band-gap nature of graphene. Finite element studies showed that the by introducing the inevitable dislocation, mono atom vacancy and Stone–Wales defects to GQD models, their mechanical properties reduces to approach data from experimental investigations, whereas an increase in the number of layers does not influence the obtained results significantly.