This paper outlines a system level safety analysis procedure for research reactors incorporating sensitivity and uncertainty components. The protected loss of flow (LOF) accident was selected as an exemplified design basis accident to demonstrate the analysis procedure. The conceptual NIST (National Institute of Standards and Technology) horizontally split-core based research reactor was adopted as a research reactor model in the study. Two system level dynamics codes, RELAP5-3D and PARET, were employed in this work in a comparison study manner. The primary objective of the present work is to demonstrate the analysis capability of integrating sensitivity and uncertainty information in addition to traditional predictions of the system code models for the study of the thermal-hydraulics (T/H) safety characteristics of research reactors under accidental transient scenarios. The canonical transient predictions on the LOF accident yielded from the two system codes mentioned above have demonstrated some noticeable yet acceptable discrepancies. To better understand the discrepancies observed in the simulations, sensitivity and uncertainty analyses were performed by coupling the RELAP5-3D model and the data analytic engines provided by the RAVEN framework developed by INL. The sensitivity information reveals the significances of key figure of merits such as the peak cladding temperature varies with different boundary and initial parameters in both normal operation and design basis transients. The uncertainty analysis informs the deviations of the responses contributed by the errors of various input components. Both the sensitivity and uncertainty information will be incorporated into a safety analysis framework as part of the safety characteristic predictions delivered by the framework.