Occlusal discoloration due to staining frequently occurs on the pits and fissures of teeth. Noncariogenic discoloration (non-CD) refers to the attachment of staining chromogens to sound surfaces, whereas cariogenic discoloration (CD) represents the discoloration of porous structures due to bacterial metabolites and mineral loss from the enamel surface. This study evaluated whether it is possible to distinguish between non-CD and CD on stained occlusal surfaces with fluorescence assessed by the quantitative light-induced fluorescence (QLF) technology. Sixty-two extracted human permanent teeth with suspected discolorations on the pit and fissure were examined. The maximum values of fluorescence loss (ΔFmax) and red fluorescence gain (ΔRmax) were calculated using QLF images. Using histology as the gold standard, it was found that 12 teeth were sound (non-CD), while 50 teeth had enamel and dentine caries (CD). The validity tests at the enamel histological caries level, ΔRmax (ρ  =  0.80) were strongly correlated with the histology (P  <  0.001). At the optimum threshold (105.0) of ΔRmax, it showed high levels of sensitivity and specificity (0.96 and 0.83, respectively). Therefore, QLF can be used to distinguish non-CD from CD on occlusal surfaces using red fluorescence values with high validity.