Single Flux Quantum (SFQ) digital logic enables power-efficient high performance computing for quantum computing, neural networks, and space applications. However, scalability is hindered by high area overhead from gate-level path balancing and large splitter trees requiring excessive pipelining. Prior attempts to reduce area using multi-phase clocking and asynchronous designs have led to substantial throughput reductions, undermining SFQ’s performance advantages. To address this, we propose a timing-aware circuit optimization method that reduces area without sacrificing performance. Our approach accounts for gate delays while jointly optimizing splitter tree topology and gate-level clocking assignments to efficiently pipeline datapaths, achieving high performance with reduced area. Applied to multi-phase clocking, it relaxes strict path balancing constraints while maintaining full path balancing performance. Experimental results on benchmark circuits show a 34% area reduction at 50 GHz compared to prior FPB methods, while timing-aware multi-phase clocking achieves a 27% area reduction and a 30% latency reduction compared to 33 GHz FPB. These results highlight the potential for integrating timing-aware synthesis with physical design methodologies to further optimize SFQ circuits. Future work aims to incorporate wire delays and predictive placement for improved scalability and performance.