The influence of the Sc cation substituent on the structural and luminescence properties of GAGG:Ce crystals was studied. Unit cell parameters and space groups were obtained using XRD analysis. The chemical compositions of the crystals were determined using SEM-EDX and TEM-EDX techniques. Structures were refined by the Rietveld method and the distribution of Al/Ga/Sc cations between octahedral and tetrahedral sites was obtained. The influence of Sc on the electronic band structure and the energy of the 4f and 5d Ce3+ levels is shown. The modification of the band structure induced by the Sc electronic states results in the suppression of Gd emission and enhancement of Ce3+ emission at low temperatures. The Ce3+ emission decay is accelerated under high-energy excitation of the Sc-containing GAGG compound.