Francisella tularensis is a Gram-negative intracellular bacterium which causes the zoonotic disease called tularemia, and a potential bioterror weapon. Francisella tularensis subsp. novicida can activate mammalian innate immune signalling pathways such as inflammasomes. Inflammasomes are cytosolic signalling complexes capable of sensing microbial ligands to trigger inflammation and cell death responses. We and others have shown that IFN-inducible GTPases, including the guanylate-binding proteins (GBPs) can contribute to inflammasome responses. How each member of the GBP family, which comprises 11 GBPs in mice and 7 in humans, discriminates microbes and cooperates with one another to drive pathogen-selective inflammasome responses has remained largely unclear. Here, we show that F. novicida can be targeted by mouse GBPs leading to inflammasome activation. In particular, GBP1 and GBP3 are specifically required for the activation of inflammasome in response to F. novicida infection but not to other bacterial pathogens including Listeria monocytogenes, Salmonella enterica serovar Typhimurium, Escherichia coli and Citrobacter rodentium. We further show that the intracellular proliferation of F. novicida is restricted by GBP1 and GBP3 in primary mouse macrophages. Additionally, we show that GBP1 and GBP3 provide mice protection against F. novicida infection. Our results reveal that GBPs discriminate between pathogens and confer activation of innate immunity.