Raman and surface-enhanced Raman scattering (SERS) of 5-fluorouracil (5-FU) have been recorded under several experimental conditions. SERS spectra have been analysed according to a resonant charge-transfer (CT) mechanism similar to a resonance Raman (RR) process, involving the photoinduced transfer of an electron from the Fermi level of the metal to vacant orbitals of the adsorbate (SERS-CT). In order to detect the enhancement mechanism and to identify the chemical species that give rise to the spectra, the theoretical SERS-CT intensities for the dienolic and diketo forms, and its respective N1 and N3 deprotonated anions (5-FU−), have been calculated and compared with the experimental results. In this way, the presence of N1 deprotonated anion is confirmed by SERS given that the calculated SERS-CT intensities predict the selective enhancement of the band at ca. 1680 cm−1 in agreement with the experiment. Therefore, the metal-to-adsorbate CT process involves the transient formation of the respective radical dianion (5-FU˙2−), which is new evidence of the relevance of the CT enhancement mechanism in SERS.