This paper proposes a novel methodology to synthesize highly fluorescent gold nanoparticles (NPs) with a maximum quantum yield of 16%, in the near-infrared (IR) region. This work discusses the results of using our (previously developed) matrix sputtering method to introduce mercaptan molecules, alpha-thioglycerol, inside the vacuum sputtering chamber, during the synthesis of metal NPs. The evaporation of alpha-thioglycerol inside the chamber enables to coordinate to the nucleation stage very small gold nanoclusters in the gas phase, thus retaining their photophysical characteristics. As observed through transmission electron microscopy, the size of the Au NPs obtained with the addition of alpha-thioglycerol varied from approximately 23 nm to approximately 5 nm. Plasmon absorption varied with the size of the resultant nanoparticles. Thus, plasmon absorption was observed at 2.4 eV in the larger NPs. However, it was not observed, and instead a new peak was found at approximately 3.4 eV, in the smaller NPs that resulted from the introduction of alpha-thioglycerol. The Au NPs stabilized by the alpha-thioglycerol fluoresced at approximately 1.8 eV, and the maximum wavelength shifted toward the red, in accordance with the size of the NPs. A maximum fluorescent quantum yield of 16% was realized under the optimum conditions, and this value is extremely high compared to values previously reported on gold NPs and clusters (generally similar to 1%). To our knowledge, however, Au NPs of size >2 nm usually do not show strong fluorescence. By comparison with results reported in previous literature, it was concluded that these highly fluorescent Au NPs consist of goldmercaptan complexes. The novel method presented in this paper therefore opens a new door for the effective control of size, photophysical characteristics, and structure of metal NPs. It is hoped that this research contributes significantly to the science in this field.