Small gold nanorods have a significantly large absorption/scattering ratio and are especially beneficial in exploiting photothermal effects, for example in photothermal therapy and remote drug release. This work systematically investigates the influence of growth conditions on the size, growth yield, and stability of small gold nanorods. The silver-assisted seed-mediated growth method was optimized to synthesize stable small gold nanorods with a high growth yield (>85%). Further study on the influence of silver ions on the growth facilitates the growth of small gold nanorods with tunable longitudinal surface plasmon resonance from 613 to 912 nm, with average dimensions of 13-25 nm in length and 5-6 nm in diameter. Moreover, the small gold nanorods were successfully functionalized with thiol-modified hairpin oligonucleotides (hpDNA) labeled with Cy5. Fluorescence intensity measurements show an increase in the presence of target DNA and an enhanced signal/background ratio when the longitudinal surface plasmon resonance of small gold nanorods overlaps with the excitation and emission wavelength of Cy5. This coincides with a reduced fluorescence lifetime of Cy5 in the hairpin structure, indicating surface plasmon resonance-enhanced energy transfer to the small gold nanorods. This study may provide insight on the synthesis and functionalization of small gold nanorods in biomedical sensing and therapy.