The estimation of failure probability is challenging in hydrogen embrittlement in steel pipelines due to the complexity of the synergistic effect of multiple factors. The present study proposed a hybrid methodology to estimate the failure probability of steel pipelines due to hydrogen embrittlement. The methodology integrates the fault tree analysis with a fuzzy comprehensive evaluation. Fault tree analysis captures the logical relationships between influencing indicators to develop a new assessment model of hydrogen embrittlement in steel pipelines. An improved fuzzy fault tree analysis method was proposed to process aleatoric and epistemic uncertainties to estimate the probability of each basic event due to the difficulty in obtaining the actual probabilities. The failure probability of blended hydrogen natural gas pipelines was estimated by considering the correlation of events. A case study demonstrated the applicability of the proposed method. Maintenance measures can be implemented according to the evaluation results to ensure pipeline safety.