Apparatus and method for replacing portions of a quantum circuit with multi-qubit gates. For example, one embodiment of an apparatus comprises: a quantum circuit analyzer to evaluate an original quantum circuit specification including one or more sub-circuits of the original quantum circuit specification, the quantum circuit analyzer to generate results of the evaluation; a quantum circuit generator to generate a new quantum circuit specification based on the results of the evaluation generated by the quantum circuit analyzer, the quantum circuit generator to generate the new quantum circuit specification by, at least in part, replacing the one or more sub-circuits of the original quantum circuit specification with one or more multi-qubit gates.