As grid energy storage systems become more complex, it grows more difficult to design them for safe operation. This paper first reviews the properties of lithium-ion batteries that can produce hazards in grid scale systems. Then the conventional safety engineering technique Probabilistic Risk Assessment (PRA) is reviewed to identify its limitations in complex systems. To address this gap, new research is presented on the application of Systems-Theoretic Process Analysis (STPA) to a lithium-ion battery based grid energy storage system. STPA is anticipated to fill the gaps recognized in PRA for designing complex systems and hence be more effective or less costly to use during safety engineering. It was observed that STPA is able to capture causal scenarios for accidents not identified using PRA. Additionally, STPA enabled a more rational assessment of uncertainty (all that is not known) thereby promoting a healthy skepticism of design assumptions. We conclude that STPA may indeed be more cost effective than PRA for safety engineering in lithium-ion battery systems. However, further research is needed to determine if this approach actually reduces safety engineering costs in development, or improves industry safety standards.