This main focus of this study was to evaluate the thermal degradation kinetics and the phytochemical characterization of the elderberries extract. Pelargonidin-3-sophoroside and delphinidin-3-glucoside were identified as the major anthocyanin compounds and catechin hydrate as the major flavonoid compound. In order to further understand the action of the heat treatment on the bioactive compounds from elderberry extract, fluorescence studies were also carried out. In general, heating at temperatures ranging from 100 to 150 ℃ for up to 90 min caused a decrease in fluorescence intensity, simultaneously with significant redshifts in λmax suggesting important molecular changes inside the anthocyanins structure, affecting the antioxidant activity. Increasing the heating time up to 120 min, the elderberry extract peaked at about 88 nm shifted toward higher wavelengths with respect to that of untreated solutions (peak at 442 nm). The kinetics studies of anthocyanins, fluorescence intensity, and antioxidant activity evidenced a decrease of the degradation rate constants with increased temperature while the activation energies for heat-induced fluorescence intensity, monomeric anthocyanins, and antioxidant activity were 39.62 ± 9.60, 49.97 ± 5.61, and 31.04 ± 19.92 kJ/mol, respectively. Our results can be valuable in terms of establishing the appropriate processing and formulation protocols that could lead to a more efficient utilization of these pigments in actual food products and/or nutraceuticals.