Candida species are the commensal organisms of human mucosa and opportunistically cause the diseases in susceptible persons. This study aimed to determine the prevalence and virulence of different Candida spp. among nephrolithiatic patients and their association with complicated UTI (cUTI). A total of 164 urine samples were collected from surgical units of two tertiary care hospitals (Poly Clinic and Pakistan Institute of Medical Sciences Hospital, Islamabad). From 74 kidney stone patients, 77 isolates of Candida spp. were confirmed through standard microbiological and molecular characterization. C. albicans was the predominant species with 51 isolates (66.2%) followed by 26 (33.8%) of C. non-albicans. The nephrolithiatic patients suffering from cUTI were more prone to be infected with Candida (P=0.047). Among all isolates, 83% (64) of the Candida isolates were biofilm formers, 80% (60) showed the esterase production and 64.9% (50) showed phospholipase production. Candida isolates positive for various virulence factors were more prevalently isolated from both catheterized and recurrent UTI patients. Among Candida spp., 16.9% (13) isolates showed resistance to fluconazole and 19.5% (15) against voriconazole and 11 isolates were resistant for both tested antifungals. Candida isolated from cUTI cases showed comparatively enhanced virulence attributes and antifungal resistance, suggesting that these factors might have role in development of cUTI in nephrolithiatic patients. Hence, this work highlights the high prevalence of both C. albicans and non albicans spp. in nephrolithiatic patients. So, there is need to administer evidence based antifungal therapy rather than empirical therapy to reduce the cUTI in nephrolithiatic patients.