The last two decades have witnessed major advances in the synthesis and characterization of endohedral fullerenes. These species have interesting physicochemical properties with many potential interesting applications in the fields of magnetism, superconductivity, nonlinear optical properties, radioimmunotherapy, and magnetic resonance imaging contrast agents, among others. In addition to the synthesis and characterization, the chemical functionalization of these species has been a main focus of research for at least four reasons: first, to help characterize endohedral fullerenes that could not be well described structurally otherwise; second, to generate materials with fine-tuned properties leading to enhanced functionality in one of their multiple potential applications; third, to produce water-soluble endohedral fullerenes needed for their use in medicinal sciences; and fourth, to generate electron donor–acceptor conjugates that can be used in solar energy conversion/storage. The functionalization of these species has been achieved through different types of reactions, the most common being the Diels–Alder reactions, 1,3-dipolar cycloadditions, Bingel–Hirsch reactions, and free-radical reactions. It has been found that the performance of these reactions in endohedral fullerenes may be quite different from that of the empty fullerenes. Indeed, encapsulated species have a large influence on the thermodynamics, kinetics, and regiochemistry of these reactions. A detailed understanding of the changes in chemical reactivity due to incarceration of atoms or clusters of atoms is essential to assist the synthesis of new functionalized endohedral fullerenes with specific properties. This Perspective seeks to highlight the key role played by computational chemistry in the analysis of the chemical reactivity of these systems. It is shown that the information obtained through calculations is highly valuable in the process of designing new materials based on endohedral fullerenes.