Generation of triplet excited states through radical pair intermediates has been extensively studied in molecular complexes. Similar schemes remain rare in hybrid structures of quantum dot-organic molecules, despite intense recent interest of quantum dot sensitized triplet excited state generation. Herein, we demonstrate that the efficiency of the intersystem crossing from the singlet to the triplet state in boron dipyrromethene (BODIPY) can be enhanced in CdSe quantum dot-BODIPY complexes through a radical pair intermediate state consisting of an unpaired electron in the quantum dot conduction band and that in oxidized BODIPY. By transient absorption spectroscopy, we show that the excitation of BODIPY with 650 nm light leads to the formation of a charge separated state by electron transfer from BODIPY to CdSe (with a time constant of 6.33 ± 1.13 ns), competing with internal conversion to the ground state within BODIPY, and the radical pair state decays subsequently by back charge recombination to generate a triplet excited state (with a time constant of 158 ± 28 ns) or the ground state of BODIPY. The overall quantum efficiency of BODIPY triplet excited state generation was determined to be (27.2 ± 3.0)%. The findings of efficient triplet state formation and intermediate radical pair states in this hybrid system suggest that quantum dot-molecule complexes may be a promising platform for spintronics applications.