Abstract This paper introduces SuperSIM, a benchmarking framework tailored for neural networks using superconducting Josephson devices, specifically focusing on Adiabatic Quantum Flux Parametron (AQFP) based Processing-in-Memory (PIM) architectures. Our framework offers in-depth architecture-level simulations and performance assessments to enhance AQFP PIM chip development. It supports single and multi-bit PIM designs, various AQFP memory cell types, and diverse clocking methods. Additionally, it integrates circuit-level models for precise energy, delay, and area measurements, ensuring accurate performance evaluation. The framework includes application, device, and architectural layers for versatile configurations and cycle-accurate energy, latency, and area simulations. Experiments validate our framework, with case studies on algorithm and architecture-level features, examining data precision, crossbar size, operating frequency and clocking scheme impacts on computational accuracy, energy use, overall latency and hardware cost.