Physical superconducting qubits are controlled according to an “encoded” qubit scheme, where a pair of physical superconducting qubits constitute an encoded qubit that can be controlled without the use of a microwave signal. For example, a quantum computing system has at least one encoded qubit and a controller. Each encoded qubit has a pair of physical superconducting qubits capable of being selectively coupled together. Each physical qubit has a respective tunable frequency. The controller controls a state of each of the pair of physical qubits to perform a quantum computation without using microwave control signals. Rather, the controller uses DC-based voltage or flux pulses.