In this study, a 4-year-old girl presented with a case of septic arthritis and fever. Salmonella was isolated from her knee effusion and feces; isolates were confirmed to be a novel S. Virchow monophasic variant (Salmonella 6,7,14:r:-) based on core genome MLST (cgMLST), CRISPR typing combined with analysis of the fljAB operon. Whole-genome sequencing analysis revealed that replacement of the fljAB operon by a 4.8 kb cassette from E. coli caused the nonexpression of phase-2 flagellar antigen in S. Virchow monophasic variant. Additionally, the acquisition of Salmonella genomic island 2 (SGI2) with an antimicrobial resistance gene cassette enabled the isolates to be multidrug-resistant (MDR) to chloramphenicol, tetracycline, trimethoprim, and sulfamethoxazole. The emerging of MDR S. Virchow monophasic variant causing human infection should be concerned in the national Salmonella surveillance system.