The excitation-related problems in photodynamic therapy of cancer might be solved by combining two-photon (TP) irradiation and quantum dots (QDs) as effective energy donors for conventional photosensitizers (PS). Here, it is demonstrated for the first time that QD-chlorin e6 (Ce6) complex formed due to the hydrophobic interaction between Ce6 molecules and lipid coating of QDs can be effectively excited via TP irradiation at 1030 nm, which spectrally coincides with the biological tissue optical window. TP absorption cross-section for free QDs and Ce6 at 1030 nm was 3325 and 13 Goeppert-Mayer, respectively. Upon TP excitation of QD-Ce6 solution, the fluorescence band of bound Ce6 molecules was observed via energy transfer from excited QDs. Increasing concentration of Ce6 resulted in quenching of the photoluminescence of QDs and an increase in the fluorescence intensity of bound Ce6 molecules. These intensity changes coincided well with those observed upon single-photon excitation of QD-Ce6 solution when QDs alone are excited. The efficiency of energy transfer in QD-Ce6 complex upon TP excitation was about 80% (QD∶Ce61∶5). These results indicate that the effective excitation of PS with a low TP absorption cross-section is possible in such type noncovalent complexes via energy transfer from TP excited QDs.