The semiconductor industry seeks energy-efficient alternatives as Moore’s law nears its limits. The Single Flux Quantum (SFQ) integrated circuits (ICs) using thousands of niobium Josephson junctions (JJs) and operating at 4 K show great promise for digital computing circuits at high speed (>20 GHz) and low power (a few nW per junction). The leading logic families are Rapid Single Flux Quantum (RSFQ), and its energy-efficient variant (ERSFQ). IARPA’s SuperTools program aims to develop integrated design tools for superconductor electronics, targeting SFQ and Adiabatic Quantum-Flux-Parametron (AQFP) logic families. This paper presents a passive transmission line (PTL) based standard cell library for SFQ logic, designed with Synopsys Electronic Design Automation (EDA) software tools for MIT-LL 100μA/μm2 SFQ5ee fab node. The dual RSFQ/ERSFQ standard cell library facilitates seamless integration of SFQ RTL-to-GDS design flow with Synopsys Fusion Compiler, an automated design tool. The SFQ RTL-to-GDS flow entails logic synthesis, checking, placement, clock synthesis, and routing. Row-based placement for library cells and H-tree clock tree structures are employed. Fusion Compiler’s effectiveness is validated with Hypres designs such as finite impulse response (FIR) filters, scalable multiply-accumulate (MAC) units, and memory arrays, comparing single and dual clocking schemes. The synergy between Hypres and Synopsys achieves a milestone by demonstrating the design of a digital superconducting circuit with over 10 million JJs, facilitated by a fully automated design tool for the first time. Challenges in very large-scale SFQ scaling are also discussed.