A 70-year-old woman presented to our hospital with 38.2 °C fever. She was diagnosed with high-risk emphysematous pyelonephritis caused by string test-positive Klebsiella pneumoniae and treated with multidisciplinary therapy. The patient developed pyogenic spondylitis during the course of the disease. This is the first reported case of emphysematous pyelonephritis caused by the hypermucoviscosity phenotype of K. pneumoniae and the second reported case of pyogenic spondylitis. The hypermucoviscosity phenotype of K. pneumoniae should be considered as an etiologic agent of emphysematous pyelonephritis.