Realistic quantum computing is subject to noise. Therefore, an important frontier in quantum computing is to implement noise-resilient quantum control over qubits. At the same time, dynamical decoupling can protect the coherence of qubits. Here we demonstrate non-trivial quantum evolution steered by dynamical decoupling control, which simultaneously suppresses noise effects. We design and implement a self-protected controlled-NOT gate on the electron spin of a nitrogen-vacancy centre and a nearby carbon-13 nuclear spin in diamond at room temperature, by employing an engineered dynamical decoupling control on the electron spin. Final state fidelity of 0.91(1) is observed in preparation of a Bell state using the gate. At the same time, the qubit coherence time is elongated at least 30 fold. The design scheme does not require the dynamical decoupling control to commute with the qubit interaction and therefore works for general qubit systems. This work marks a step towards implementing realistic quantum computing systems.