A two-dimensional monolayer of silicon atoms, called silicene, is similar to graphene, yet arranged in a hexagonal buckled lattice. By replacing all the silicon-28 atoms in silicene with other stable silicon isotopes, i.e. silicon-29 and silicon-30, it is possible to engineer the band structure of silicene and thus making it a potential material for an isotopic homojunction, which means that a “heterostructure” can be formed by replacing atoms in the unit cell with their isotope counterparts. In this study, we investigate the effect of different silicon isotopes on the band structure of silicene by first-principles calculations. We find that there might be a change in the lattice constant of silicene due to the isotopic substitution and thus the electronic energy dispersion can be modified in the order of meV. In the case of the phonon dispersion, the isotope mass will give a dominant contribution to shifting the phonon frequency.