Pseudomonas aeruginosa (P. aeruginosa) is a gram-negative aerobic bacterium, which is rarely seen in community-acquired infection. Attention should be paid to its high mortality and invasive progress. X-linked hyper-IgM syndrome (XHIGM; HIGM1; OMIM:308230) is one type of primary immunodeficiency disease (PIDs), characterized by markedly decreased serum IgG, IgA, and IgE levels and normal or elevated serum IgM levels. We report a patient who developed a particularly severe community-acquired P. aeruginosa pneumonia-related septic shock, and a delayed diagnosis of X-linked hyper IgM syndrome was made by genome sequencing. Fatal community-acquired P. aeruginosa infections in children, including previously healthy children, should be considered to search for underlying PIDs by exome/genome sequencing.