Conventional semiconductor-based integrated circuits are gradually approaching fundamental scaling limits. Many prospective solutions have recently emerged to supplement or replace both the technology on which basic devices are built and the architecture of data processing. Neuromorphic circuits are a promising approach to computing where techniques used by the brain to achieve high efficiency are exploited. Many existing neuromorphic circuits rely on unconventional and useful properties of novel technologies to better mimic the operation of the brain. One such technology is single flux quantum (SFQ) logic—a cryogenic superconductive technology in which the data are represented by quanta of magnetic flux (fluxons) produced and processed by Josephson junctions embedded within inductive loops. The movement of a fluxon within a circuit produces a quantized voltage pulse (SFQ pulse), resembling a neuronal spiking event. These circuits routinely operate at clock frequencies of tens to hundreds of gigahertz, making SFQ a natural technology for processing high frequency pulse trains. This work harnesses thermal stochasticity in superconducting synapses to emulate stochasticity in biological synapses in which the synapse probabilistically propagates or blocks incoming spikes. The authors also present neuronal, fan-in, and fan-out circuitry inspired by the literature that seamlessly cascade with the synapses for deep neural network construction. Synapse weights and neuron biases are set with bias current, and the authors propose multiple mechanisms for training the network and storing weights. The network primitives are successfully demonstrated in simulation in the context of a rate-coded multi-layer XOR neural network which achieves a wide classification margin. The proposed methodology is based solely on existing SFQ technology and does not employ unconventional superconductive devices or semiconductor transistors, making this proposed system an effective approach for scalable cryogenic neuromorphic computing.