We demonstrate a two-qubit logic gate driven by near-field microwaves in a room-temperature microfabricated ion trap. We measure a gate fidelity of 99.7(1)%, which is above the minimum threshold required for fault-tolerant quantum computing. The gate is applied directly to $^{43}$Ca$^+$ atomic clock qubits (coherence time $T_2^*approx 50,mathrm{s}$) using the microwave magnetic field gradient produced by a trap electrode. We introduce a dynamically-decoupled gate method, which stabilizes the qubits against fluctuating a.c. Zeeman shifts and avoids the need to null the microwave field.