Apparatus and method for a full quantum system simulator. For example, one embodiment of a method comprises: initializing a quantum computing system simulator for simulating multiple layers of a quantum system including one or more non-quantum layers and one or more physical quantum device layers of the quantum system; simulating a first set of operations of the one or more non-quantum layers of the quantum system to generate first simulation results; simulating a second set of operations of the one or more quantum device layers of the quantum system to generate second simulation results; analyzing the first and second simulation results to provide at least one configuration recommendation for the quantum system.