Eu3+ and Li+ ion co-doped fluorapatite (Ca10(PO4)6F2) nanocrystals were fabricated using a microwave stimulated hydrothermal technique followed by heat treatment at 500 °C. The concentration of Eu3+ ions was set to be 1 mol% and that of the Li+ ions was in the range of 0.5–5 mol% to investigate the site occupancy preference and charge compensation co-doping. The structural and morphological properties of the obtained samples were determined by using XRD (X-ray powder diffraction) and TEM (transmission electron microscopy) techniques as well as IR (infrared) and micro-Raman spectroscopy. The particle size was verified and calculated by the Rietveld method being in the range of 70–95 nm. The luminescence properties (the emission, excitation spectra and emission kinetics) of the Eu3+ ion-doped fluorapatite depending on the co-dopant (Li+ ions) were recorded. Significantly, fluorescence quenching by OH− groups was eliminated by F- ions and the luminescence intensity was enhanced by co-doping with Li+ ions. The simplified Judd–Ofelt (J–O) theory has been performed to explain a detailed analysis of the luminescence spectra.