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The realization of strong photon–photon interactions has presented an enduring challenge across photonics, particularly in quantum computing, where two-photon gates form essential components for scalable quantum information processing (QIP). While linear-optic schemes have enabled probabilistic entangling gates in spatio-polarization encoding, solutions for many other useful degrees of freedom remain missing. In particular, no two-photon gate for the important platform of frequency encoding has been experimentally demonstrated, due in large part to the additional challenges imparted by the mismatched wavelengths of the interacting photons. In this article, we design and implement an entangling gate for frequency-bin qubits, a coincidence-basis controlled-NOT (CNOT), using line-by-line pulse shaping and electro-optic modulation. We extract a quantum unitary fidelity of 0.91 ± 0.01 via a parameter inference approach based on Bayesian machine learning, which enables accurate gate reconstruction from measurements in the two-photon computational basis alone. Our CNOT imparts a single-photon frequency shift controlled by the frequency of another photon—an important capability in itself—and should enable new directions in fiber-compatible QIP.