Zeolites have been proposed as carrier materials for the encapsulation and controlled release of the anticancer drug 5-fluorouracil (5-FU). Besides, they could also find use in the adsorption-based removal of 5-FU from water, for example in the treatment of hospital effluents. In the present work, dispersion-corrected density functional theory (DFT) calculations and DFT-based ab initio molecular dynamics (AIMD) simulations are employed to study the interaction of 5-FU with faujasite-type zeolites having different Si/Al ratios. Comparing distinct local arrangements of Al atoms and charge-balancing protons, it is evaluated to what extent “multi-site” interactions, i.e., interactions of 5-FU with more than one proton, affect the adsorption energy. Additionally, infrared spectra are predicted for selected low-energy configurations in order to facilitate an experimental identification of different bonding environments. Typically, several hydrogen bonds are formed between 5-FU and the framework, and the stability of these bonds at room temperature is probed with AIMD simulations. While they are largely stable in the absence of water, competitive adsorption of water molecules results in a breaking of hydrogen bonds, framework deprotonation, and a displacement of 5-FU from its initial position. Exposure of dehydrated 5-FU@FAU composites to water might thus be a useful approach to trigger 5-FU release in drug delivery applications.