In this work, the electronic, thermochemical, and vibrational characterization of the drug delivery system formed by clusters of selenium (Se₆ allotrope) and 5-fluorouracil (5-FU) are studied, based on density functional theory (DFT) calculations. Computational calculations were performed using the B3LYP functional and the 6-31G(d,p) base set, considering an aqueous medium through the CPCM solvation model. We propose evaluating two different interaction modes based on experimental observations: Se–H(N) (through the amino groups of 5-FU) and Se–O(C) (through the carbonyl oxygen of 5-FU). All complexes proved to be energetically stable, exhibiting chemisorption as their adsorption process. Analysis of adsorption energy and thermodynamic parameters indicates that both interaction pathways are equally viable, which agrees with previous experimental findings. The theoretical FT-IR spectra of these complexes also coincide with the experimental results. Furthermore, global molecular descriptors show that the stability of the selenium carrier is not affected by post-functionalization, which is desirable for more controlled drug delivery systems.