An uncertainty analysis is required to be carried out in formal safety assessment (FSA) by the International Maritime Organization. The purpose of this article is to introduce the uncertainty analysis technique into the FSA process. Based on the uncertainty identification of input parameters, probability and possibility distributions are used to model the aleatory and epistemic uncertainties, respectively. An approach which combines the Monte Carlo random sampling of probability distribution functions with the a-cuts for fuzzy calculus is proposed to propagate the uncertainties. One output of the FSA process is societal risk (SR), which can be evaluated in the two-dimensional frequency–fatality (FN) diagram. Thus, the confidence-level-based SR is presented to represent the uncertainty of SR in two dimensions. In addition, a method for time window selection is proposed to estimate the magnitude of uncertainties, which is an important aspect of modeling uncertainties. Finally, a case study is carried out on an FSA study on cruise ships. The results show that the uncertainty analysis of SR generates a two-dimensional area for a certain degree of confidence in the FN diagram rather than a single FN curve, which provides more information to authorities to produce effective risk control measures.