Apparatus and method for dynamically adjusting a quantum computer clock frequency. For example, one embodiment of an apparatus comprises: a quantum execution unit to execute quantum operations specified by a quantum runtime; a qubit drive controller to translate the quantum operations into physical pulses directed to qubits on a quantum chip at a first cycle frequency; a spin echo sequencer to issue spin echo command sequences to cause the qubit drive controller to generate a sequence of spin echo pulses at the first cycle frequency; and qubit measurement circuitry to measure the qubits and to store qubit timing data for each qubit, the qubit timing data indicating a coherence time or an amount of computational time available for each qubit to perform quantum operations.