As LLMs become increasingly prevalent across various applications, it is critical to establish safety guardrails to moderate input/output content of LLMs. Existing guardrail models treat various safety categories independently and fail to explicitly capture the intercorrelations among them. This has led to limitations such as ineffectiveness due to inadequate training on long-tail data from correlated safety categories, susceptibility to jailbreaking attacks, and inflexibility regarding new safety categories. To address these limitations, we propose $R^2$-Guard, a robust reasoning enabled LLM guardrail via knowledge-enhanced logical reasoning. Specifically, $R^2$-Guard comprises two parts: data-driven category-specific learning and reasoning components. The data-driven guardrail models provide unsafety probabilities of moderated content on different safety categories. We then encode safety knowledge among different categories as first-order logical rules and embed them into a probabilistic graphic model (PGM) based reasoning component. The unsafety probabilities of different categories from data-driven guardrail models are sent to the reasoning component for final inference. We employ two types of PGMs: Markov logic networks (MLNs) and probabilistic circuits (PCs), and optimize PCs to achieve precision-efficiency balance via improved graph structure. To further perform stress tests for guardrail models, we employ a pairwise construction method to construct a new safety benchmark TwinSafety, which features principled categories. We demonstrate the effectiveness of $R^2$-Guard by comparisons with eight strong guardrail models on six safety benchmarks, and demonstrate the robustness of $R^2$-Guard against four SOTA jailbreaking attacks. $R^2$-Guard significantly surpasses SOTA method LlamaGuard by 30.2% on ToxicChat and by 59.5% against jailbreaking attacks.