The Q fever agentCoxiella burnetiiuses a defect in organelle trafficking/intracellular multiplication (Dot/Icm) type 4b secretion system (T4SS) to silence the host innate immune response during infection. By investigatingC. burnetiieffector proteins containing eukaryotic-like domains, here we identify NopA (nucleolar protein A), which displays four regulator of chromosome condensation (RCC) repeats, homologous to those found in the eukaryotic Ras-related nuclear protein (Ran) guanine nucleotide exchange factor (GEF) RCC1. Accordingly, NopA is found associated with the chromatin nuclear fraction of cells and uses the RCC-like domain to interact with Ran. Interestingly, NopA triggers an accumulation of Ran-GTP, which accumulates at nucleoli of transfected or infected cells, thus perturbing the nuclear import of transcription factors of the innate immune signaling pathway. Accordingly, qRT-PCR analysis on a panel of cytokines shows that cells exposed to theC. burnetii nopA::Tn or a Dot/Icm-defectivedotA::Tn mutant strain present a functional innate immune response, as opposed to cells exposed to wild-typeC. burnetiior the correspondingnopAcomplemented strain. Thus, NopA is an important regulator of the innate immune response allowingCoxiellato behave as a stealth pathogen.