Recently, vancomycin-resistant strains have emerged as a significant threat to patients. This study describes the local epidemiological trend of vancomycin-resistant E. faecium (VR-E. faecium) strains isolated from urine, their antibiotic susceptibility to empirical treatment, patients and wards at increased risk. We retrospectively analyzed E. faecium isolates collected from January 2013 to December 2020 as part of standard patient care at the University Hospital of Bari, Italy. The antimicrobial susceptibility of E. faecium was assessed using an automated system. Out of 512 E. faecium isolates, 110 (21.48%, 95% CI: 18.06%-25.35%) were vancomycin-resistant. A relevant increase of resistance rates to vancomycin (1.45% Vs 21.48% Vs 38.78%, p-value <0.001, Cramer’s V= 0.282) was observed during years 2013-2015, 2016-2017, and 2018-2020. A linearly increasing trend of vancomycin resistance rates was observed (p-value <0.001). The VR-E. faecium isolates were multidrug-resistant with resistance versus quinupristin/dalfopristin (9.18%) and linezolid (3.56%). A VanA phenotype was observed in 95.45% VR-E.faecium strains. The maximum prevalence of VR-E. faecium strains were found in the ICU. Vancomycin resistance was associated with the patient’s age. This retrospective analysis of urinary E. faecium isolates revealed a progressive increase of vancomycin resistance that highlights the need for an active surveillance system and control strategies to avoid outbreaks inwards with critically ill patients.