We report a spray-drying method to fabricate silver nanoparticle (AgNP) aggregates for application in surface-enhanced Raman spectroscopy (SERS). A custom-built system was used to fabricate AgNP aggregates of four sizes, 48, 86, 151, and 218 nm, from drying droplets containing AgNPs atomized from an AgNP suspension. Sample solutions of Rhodamine B (RhB) at 10–6, 10–8, and 10–10 M concentrations were dropped onto the AgNP aggregates as probe molecules to examine the enhancement of the Raman signals of the RhB. The ordering of the analytical enhancement factors (AEFs) by aggregate size at a 10–6 M RhB was 86 nm > 218 nm > 151 nm > 48 nm. When RhB concentrations are below 10–8 M, the 86 and 151 nm AgNP aggregates show clear RhB peaks. The AEFs of the 86 nm AgNP aggregates were the highest in all four aggregates and higher than those of the 218-nm aggregates, although the 218-nm aggregates had more hot spots where Raman enhancement occurred. This finding was attributable to the deformation and damping of the electron cloud in the highly aggregated AgNPs, reducing the sensitivity for Raman enhancement. When RhB was premixed with the AgNP suspension prior to atomization, the AEFs at 10–8 M RhB rose ~ 100-fold compared to those in the earlier experiments (the post-dropping route). This significant enhancement was probably caused by the increased opportunity for the trapping of the probe molecules in the hot spots.