Implementation of the two-qubit controlled-NOT (CNOT) gate is necessary to develop a complete set of universal gates for quantum computing. Here, we demonstrate that a photogenerated radical (spin qubit) pair within a covalent donor-chromophore-acceptor molecule can be used to successfully execute a CNOT gate with high fidelity. The donor is tetrathiafulvalene (TTF), the chromophore is 8-aminonaphthalene-1,8-dicarboximide (ANI), and the acceptor is pyromellitimide (PI). Selective photoexcitation of ANI with a 416 nm laser pulse results in subnanosecond formation of the TTF•+-ANI-PI•- radical (spin qubit) pair at 85 K having a 1.8 µs phase memory time. This is sufficiently long to execute a CNOT gate using a sequence of five microwave pulses followed by a sequence of two pulses that read out all the elements of the density matrix. Comparing these data to a simulation of the data that assumes ideal conditions results in a fidelity of 0.97 for the execution of the CNOT gate. These results show that photogenerated molecular spin qubit pairs can be used to execute this essential quantum gate at modest temperatures, which affords the possibility that chemical synthesis can be used to develop structures to execute more complex quantum logic operations using electron spins.