Staphylococcus saprophyticus is second only to Escherichia coli as the most frequent causative organism of uncomplicated urinary tract infections (UTIs) among the sexually active female population. However, it is considered a rare cause of complicated UTIs in immunocompetent hosts with no identifiable risk factors for the occurrence of a complicated urinary tract infection. We report an exceedingly rare case of a 20-year-old otherwise healthy female patient, with no identifiable risk factors for complicated UTIs, who presented with a recurrent renal abscess secondary to S. saprophyticus. Serial cultures from multiple sources were negative, and the culprit organism was identified by a polymerase chain reaction (PCR) analysis of the drained pus that identified the 16 s rDNA sequences of S. saprophyticus on serial occasions. To our current date, similar cases have been rarely reported in the available literature. Our case also highlights the diagnostic value of molecular biology techniques in the identification of causative pathogens in cases of culture-negative infections when conventional microbiologic tests fail to isolate the culprit organisms. Clinical microbiology studies are needed to further explore the exact possible interactions between bacterial-specific characteristics and host-related factors that may explain the occurrence of the complicated UTIs that are associated with S. Saprophyticus among patients who are not considered to have certain risk factors that would usually predispose to complicated UTIs.