Abstract Background Globally, Candida auris is an emerging pathogen that poses an essential threat in healthcare settings presenting as outbreaks requiring significant allocation of infection control interventions to curb transmission. This fungal pathogen was initially identified in 2009 in Japan, but it has spread to all continents. Candida auris poses significant diagnostic and treatment challenges. Conventional microbiology laboratories often misidentify this pathogen as Candida haemulonii or as other Candida spp., Rhodoturola glutinis, and even with some bacterial pathogens, including Neisseria meningitidis serogroup A. Furthermore, C. auris displays distinct mechanisms of antifungal resistance to azoles and amphotericin B formulations. Most of the case series and outbreak reports have included invasive infections in adult populations. Methods Herein, we present a cluster of neonatal infections caused by Candida auris at a large referral center in Colombia. Results We report a case series of 8 neonates and infant patients who were seen at a large referral center in Colombia and who develop invasive infections caused by C. haemulonii and C. auris. Discussion Our report highlights the diagnostic challenges in identifying this fungal pathogen correctly, its clinical spectrum of disease, recommendations for empiric antifungal therapy, and it is not always associated with a high case fatality rate.