The control of cryogenic qubits in today’s super-conducting quantum computer prototypes presents significant scalability challenges due to the massive costs of generating/routing the analog control signals that need to be sent from a classical controller at room temperature to the quantum chip inside the dilution refrigerator. Thus, researchers in industry and academia have focused on designing in-fridge classical controllers in order to mitigate these challenges. Due to the maturity of CMOS logic, many industrial efforts (Microsoft, Intel) have focused on Cryo-CMOS as a near-term solution to design in-fridge classical controllers. Meanwhile, Supercon-ducting Single Flux Quantum (SFQ) is an alternative, less mature classical logic family proposed for large-scale in-fridge controllers. SFQ logic has the potential to maximize scalability thanks to its ultra-high speed and very low power consumption. However, architecture design for SFQ logic poses challenges due to its unconventional pulse-driven nature and lack of dense memory and logic. Thus, research at the architecture level is essential to guide architects to design SFQ-based classical controllers for large-scale quantum machines.In this paper, we present DigiQ, the first system-level design of a Noisy Intermediate Scale Quantum (NISQ)-friendly SFQ-based classical controller. We perform a design space exploration of SFQ-based controllers and co-design the quantum gate decompositions and SFQ-based implementation of those decompositions to find an optimal SFQ-friendly design point that trades area and power for latency and control while ensuring good quantum algorithmic performance. Our co-design results in a single instruction, multiple data (SIMD) controller architecture, which has high scalability, but imposes new challenges on the calibration of control pulses. We present software-level solutions to address these challenges, which if unaddressed would degrade quantum circuit fidelity given the imperfections of qubit hardware.To validate and characterize DigiQ, we first implement it using hardware description languages and synthesize it using state-of-the-art/validated SFQ synthesis tools. Our synthesis results show that DigiQ can operate within the tight power and area budget of dilution refrigerators at >42,000-qubit scales. Second, we confirm the effectiveness of DigiQ in running quantum algorithms by modeling the execution time and fidelity of a variety of NISQ applications. We hope that the promising results of this paper motivate experimentalists to further explore SFQ-based quantum controllers to realize large-scale quantum machines with maximized scalability.