Huanglongbing (HLB) is a devastating citrus disease caused by the phloem-resident bacterial pathogen Candidatus liberibacter asiaticus (CLas). CLas infection of susceptible varieties triggers unbalanced immune responses, leading to overaccumulation of callose and reactive oxygen species (ROS), which in turn causes phloem plugging and HLB symptom development. Interestingly, some citrus relatives exhibit little or no symptoms in the presence of CLas, a phenomenon termed HLB tolerance. Moreover, overexpression of the Arabidopsis thaliana NPR1 (AtNPR1) gene in susceptible varieties has been shown to confer robust HLB tolerance. However, the mechanisms underlying HLB tolerance remain enigmatic. Here, we show that overexpression of AtNPR1 suppresses CLas- and Pseudomonas syringae pv. maculicola ES4326 (Psm)-induced overaccumulation of callose and ROS in citrus and Arabidopsis, respectively. Importantly, we found that knocking out of the Arabidopsis negative immune regulators, AtNPR3 and AtNPR4, and silencing of their Citrus sinensis ortholog CsNPR3, similarly suppress Psm- and CLas-induced callose and ROS overaccumulation, respectively, and that silencing of CsNPR3 also enhances HLB tolerance. These results reveal a conserved role of the NPR1/NPR3/NPR4-mediated signaling pathway in regulating plant immune balances and provide mechanistic support for overexpression of AtNPR1 or silencing of AtNPR3/AtNPR4 orthologs in citrus as a long-term solution to the HLB disease.