logical qubits, which are effective qubits encoded in a high-dimensional Hilbert space. A common approach is to encode logical qubits in collective states of multiple two-level systems, but algorithms operating on multiple logical qubits are highly complex and have not yet been demonstrated. Here, we experimentally realize a controlled NOT (CNOT) gate between two multiphoton qubits in two microwave cavities. In this approach, we encode a qubit in the large Hilbert space of a single cavity mode, rather than in multiple two-level systems. We couple two such encoded qubits together through a transmon, which is driven with an RF pump to apply the CNOT gate within 190 ns. This is two orders of magnitude shorter than the decoherence time of any part of the system, enabling high-fidelity operations comparable to state-of-the-art gates between two-level systems. These results are an important step towards universal algorithms on error-corrected logical qubits.