Purpose: The high incidence of urinary tract infections (UTIs), often in nosocomial environments, is a major cause of antimicrobial resistance (AMR). The dissemination of antibiotic-resistant infections results in very high health and economic burdens for patients and healthcare systems, respectively. This study aims to determine and present the antibiotic resistance profiles of the most common pathogens in a urology department in Greece. Methods: During the period 2019–2020, we included 12,215 clinical samples of blood and urine specimens that tested positive for the following pathogens:Escherichia coli,Enterococcus faecium,Enterococcus faecalis,Proteus mirabilis,Klebsiella pneumoniae, orPseudomonas aeruginosa, as these are the most commonly encountered microbes in a urology department. Results: The analysis revealed a 22.30% mean resistance rate ofE. colistrains with a 76.42% resistance to ampicillin and a 54.76% resistance rate to ciprofloxacin in the two-year period. It also showed an approximately 19% resistance rate ofP. mirabilisstrains and a mean resistance rate of 46.205% ofK. pneumoniaestrains, with a decreasing trend during the four semesters (p-value < 0.001), which presented an 80% resistance rate to ampicillin/sulbactam and 73.33% to ciprofloxacin. The resistance to carbapenems was reported to be 39.82%. The analysis revealed a 24.17% mean resistance rate ofP. aeruginosawith a declining rate over the two-year period (p-value < 0.001). TheP. aeruginosastrains were 38% resistant to fluoroquinolones and presented varying resistance against carbapenems (31.58% against doripenem and 19.79% against meropenem). Regarding theEnteroccocalstrains, a 46.91% mean resistance was noted forE. faeciumwith 100% resistance to ampicillin, and a 24.247% mean resistance rate forE. faecalisstrains that were 41% resistant to ciprofloxacin. Both types showed 100% sensitivity to linezolid. Conclusions: The dissemination of antibiotic-resistant pathogens poses the need to implement surveillance programs and, consequently, to develop strategies to prevent the emergence of such pathogens in order to optimize patient outcomes.