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Graphene quantum dots (GQDs) was synthesized using a simple, rapid and affordable method and decorated with selenium at different molar ratios for the first time to obtain an efficient sample for use in photodynamic therapy. Surface modification of GQDs was carried out using polyethylene glycol (PEG) for conjugation with protoporphyrin IX (PpIX). Synthesized GQDs (Se: 0.3%) at 180°C had an emission spectrum that fairly coincided with the absorption profile of PpIX. A relative decrease of about 62.48% in the emission intensity of anthracene was recorded under illumination with UVC light in the presence of GQDs (Se: 0.3%) and the reduction for clung GQDs (Se: 0.3%) and PpIX during 90 min was about 70.68%. Singlet oxygen (1O2) generation was examined using a chemical method that showed significant enhancement in decomposition rate constant in clung GQDs–PEG–PpIX compared with GQDs and PpIX alone. Afterglow over 600 s showed that GQDs (Se: 0.3%) could be effective for near skin and even deep tumours.