We report the time- and symmetry-dependent surface-enhanced Raman scattering (SERS) of gold nanoparticle (AuNP) aggregates. The addition of p-aminothiophenol (p-ATP) instantly induces the aggregation of AuNPs, confirmed by large absorption in the near-IR region. Dynamic light scattering measurements show that the addition of p-ATP immediately assembles the AuNPs (13 nm) to form aggregates with a mean diameter of similar to 200 nm, which then further grow to a size of similar to 300 nm. Raman spectra acquired via time lapse show that the a(1)-symmetry bands of p-ATP are enhanced simultaneously with the formation of the aggregates, indicating that the electromagnetic enhancement largely contributes to the SERS of the AuNP aggregates. In contrast, the enhancement of the b(2)-symmetry bands occurs similar to 10 h after the formation of the aggregates and slowly progresses. The enhancement of the b(2) mode is attributed to the charge transfer between AuNPs and adsorbates, rather than the reorientation of the adsorbates because thiophenol and p-methylthiophenol that have surface structures and intermolecular interactions similar to those of p-ATP do not exhibit a symmetry-specific Raman enhancement pattern. To elucidate the disparity in the timescale between the charge-transfer resonance and the formation of the aggregates, we propose two models. A further close approach of the AuNPs constituting the aggregates causes the additional adsorption of the initially adsorbed p-ATP onto neighboring AuNPs, tuning the charge transfer state to be in resonance with the Raman excitation laser. Density functional theory calculations confirm the resonance charge-transfer tunneling through the bridging p-ATP in the AuNp-p-ATP-AuNP structures. Alternatively, the gradual continuing adsorption of p-ATP increases the local Fermi level of AuNPs into the region of resonant charge transfer from the Fermi level to the LUMO of the adsorbates. This model is corroborated by the faster appearance of b(2)-mode enhancement for the AuNPs with initially higher zeta potentials.