In this work, molecularly imprinted polymer-capped nitrogen-doped graphene quantum dots (MIP@NGQDs) were prepared via a simple sol–gel process and used for recognition of the anti-cancer drug, doxorubicin. Strong chemiluminescence (CL) emission was observed when potassium permanganate was injected into the solution of MIP@NGQDs. At the same time, in the presence of doxorubicin the CL intensity was significantly quenched and this was exploited to develop a CL detection scheme for this drug. The mechanism of the MIP@NGQDs/KMnO₄ CL system was investigated by recording UV-Vis, fluorescence and CL spectra. Under the optimal conditions, the relative CL intensity linearly decreased with the concentration of doxorubicin in the range of 20–260 μg L⁻¹. The limit of detection was 4.7 μg L⁻¹. The method was applied to the determination of therapeutic levels of doxorubicin in spiked serum samples with satisfactory results.