Here we report a novel physical approach for thiolate–protected fluorescent gold nanoparticles with a controlled size of the order of a few nanometers. This approach is based on a sputtering of gold into a liquid matrix containing thiolate ligand as a stabilizer at various concentrations, thus no reductant was used. The size of the gold nanoparticles was successfully controlled to range from 1.6 to 7.4 nm by adjusting the thiol concentrations. Surface plasmon absorption was observed in larger nanoparticles, but it was not observed in smaller ones. Such smaller nanoparticles fluoresced at around 670 nm with a small spectral shift according to their size, however, the diameter (1.6–2.7 nm) was very strange to show such red emission compared with photophysical characteristics of reported gold cluster or nanoparticles synthesized by chemical method. By detailed investigations using TEM, HAADF-STEM, XPS and TGA and size fractionation by size exclusion chromatography, we finally arrived at the plausible mechanism for the origin of unusual fluorescence property; the obtained gold nanoparticles are not single-crystal and are composed of aggregates of very small components such as multinuclear gold clusters or complexes.