Many aluminosilicate zeolites contain octahedral aluminum sites, which may occur as extra-framework or framework-associated sites. Due to the Lewis acidity of these sites, their impact on catalytic properties has been investigated frequently. Comparatively less emphasis has been placed on their role in adsorption, despite evidence for an irreversible binding of some guest molecules like the anticancer drug 5-fluorouracil (5-FU) to octahedral Al atoms. In the present study, dispersion-corrected density functional theory (DFT) calculations and DFT-based ab initio molecular dynamics simulations (AIMD) are employed to investigate the adsorption of 5-FU at a framework-associated octahedral Al site in zeolite FAU. The calculations show that 5-FU remains coordinated to the Al atom at room temperature and in the presence of water. In contrast, 5-FU molecules adsorbed at framework protons are quickly displaced by water molecules. It is thus demonstrated that octahedral Al atoms will negatively affect the release of 5-FU from zeolite hosts in drug delivery applications. A comparison of DFT-calculated infrared (IR) spectra to literature data provides evidence that Al-coordinated 5-FU molecules were indeed present in previously investigated samples.