Graphene nanoflakes (GNFs) were chosen due to their great potential for employment in electronic nanoscale applications. The most promising implementation of this paradigm is to be used as a recharging battery or as a nanosensor for various particles. The interaction between graphene nanoflakes (GNFs) and selenium or sulfur has been investigated by considering it as add atom impurity and a passivating element. The adsorption of both Se, and S at five different positions viz. hole (H), passivation (P), top (T), replace (R), and bridge (B) is studied to define the most stable structure. The electronic properties (such as band gaps, Fermi level, HOMO, and LUMO energies) and the global properties (ionization potential, electron affinity, electronegativity, hardness, softness, and electrophilicity) are calculated for GNFs with and without the Se and S atoms. All these systems were investigated by method at the B3LYP/3–21 G level in light of the density functional theory (DFT) with the Gaussian 09 program. It was detected that all the systems impinged with Selenium and Sulfur particles caused the bandgap shrinking with different values at different impurity locations. The bandgap was also affected and significantly reduced in value by the interactions of pure GNFs with impurity particles (Selenium and sulfur) with bridge denaturation. At the same time, there were slight changes in both the gap position of selenium and the passivation position of selenium and sulfur compared to the original state of GNFs.