Pantoea agglomerans is an environmental Gram-negative bacterium that rarely is responsible for the infections in humans but it is often a causative factor of a number of occupational diseases. This study evaluated the clinical and microbiological characteristics and pathogenicity of P. agglomerans in children. We retrospectively reviewed microbiological test results for all children (1 month old to 18 years old) who were admitted to our pediatric hospital between January 2000 to June 2015 and had positive clinical specimen cultures for P. agglomerans. Isolates were identified using conventional tests and the BBL Crystal E/NF ID or MALDI-TOF MS systems. Antibiotic susceptibilities were evaluated using the Kirby-Bauer disc diffusion method. We identified fifteen positive cultures from 14 patients with confirmed infections. The positive specimens included pus, urine, tracheal aspirate, blood, and central venous line samples that yielded P. agglomerans. The median patient age was 8.8 years (range: 1.5 months to 16.5 years), and all patients had underlying comorbidities. Five patients had medical devices, and two devices were removed. The most common P. agglomerans infections involved wound infections (35.7%), pneumonia (21.4%), and urinary tract infections (21.4%). Three patients had concomitant infections (Enterococcus faecium, Pseudomonas aeruginosa, and Aspergillus fumigatus). Five patients had anemia. Three patients (21.4%) died, and all three had carbapenem-resistant P. agglomerans that was detected after the first week of hospitalization; two cases involved pneumonia, which was ineffectively treated. P. agglomerans infections may be life-threatening, especially in young patients with pneumonia. Hospital-acquired P. agglomerans may have different pathogenicity and clinical features, compared to community-acquired P. agglomerans, although further studies are needed to understand the drug-resistance patterns in this bacterium.