Gold (Au) nanoclusters (NCs) are novel materials with low cytotoxicity and high chemical stability. These properties are in high demand during the bioimaging. Moreover, the optical properties of gold clusters allow to use them as colorimetric and luminescent bionanosensors. Pterins are low molecular weight organic compounds, which are used in medicine as biomarkers of phenylketonuria, vitiligo, inflammation and immune system activation, cancer, COVID-19, etc. We have investigated the possibility of gold nanosensors usage to detect pterin (Ptr). Ptr-Aunq structures (n = 1–6; q = 0–2) Gibbs energy of complexation (Eb) have been obtained using density functional theory. The highest Eb was determined for the complexes of Au62+ and Au32+ in acidic and alkaline aqueous solution, respectively. The detection of pterin with gold clusters seems to be prospective using both colorimetric and fluorescent detection because of the intense S0→S1 transition in the absorption spectrum of the Au5+ complex. Raman detection of pterin should be performed at alkaline pH because of the dramatic changes in the spectrum of Ptr−1 upon the addition of Au clusters. We believe that these tunable changes of the pterin spectra due to Au clusters and nanoparticles attachment could be exploited in further studies on nanosensor design.