Any residual coupling of a quantum computer to the environment results in computational errors. Encoding quantum information in a so-called decoherence-free subspace provides means to avoid these errors. Despite tremendous progress in employing this technique to extend memory storage times by orders of magnitude, computation within such subspaces has been scarce. Here, we demonstrate the realization of a universal set of quantum gates acting on decoherence-free ion qubits. We combine these gates to realize the first controlled-NOT gate within a decoherence-free, scalable quantum computer.