This limited-scope study demonstrates the application of probabilistic risk assessment (PRA) methodologies to a spent fuel storage system for spent pebble-filled dry cask with a focus only on the necessary PRA technical elements sufficient to risk-inform the spent fuel storage system design. A dropping canister scenario in a silo of the spent fuel storage system is analyzed through an initiating event (IE) identification from the Master Logic Diagram (MLD); event sequence analysis (ES) by establishing the event tree; data analysis (DA) for event sequence quantification (ESQ) with uncertainty quantification; mechanistic source term (MST) analysis by using ORIGEN; radiological consequence analysis (RC) by deploying MicroShield, and risk integration (RI) by showing the Frequency-Consequence (F-C) target curve in the emergency area boundary (EAB). Additionally, a sensitivity study is conducted using the ordinary least square (OLS) regression method to assess the impact of variables such as failed pebble numbers, their location in the canister, and building wall thickness. Furthermore, the release categories grouped from the end states in the event tree are verified as safety cases through the F-C curve. This study highlights the implementation of PRA elements in a logical and structured manner, using appropriate methodologies and computational tools, thereby showing how to risk-inform the design of a dry cask system for storing spent pebble-filled fuel.