Candida albicans is the most frequent cause of invasive fungal disease in preterm and/or low birth weight neonates, followed by Candida parapsilosis, whilst infections from other species are rare. Considering the severity of the disease, associated with poor clinical signs and diagnostic difficulties, primary prophylaxis becomes relevant. This paper summarizes the pathogenesis and clinical presentation of invasive candidiasis in neonates, focusing on prophylaxis. For late onset invasive disease, e.g., those occurring after the 3rd (or 7th according to some definitions) day of life possible approaches are the use of fluconazole, recommended in case of weight <1000 g or <1500 g if the local incidence of invasive candidiasis is higher than 2%, or the use of nystatin (for patients < 1500 g). Micafungin must be used in case of colonization by Candida auris, or in centers with a high prevalence of this pathogen. Concurrently, correct management of the central venous catheter and isolation procedures, with special regard to patients colonized by resistant strains, are fundamental. Other approaches such as reduced use of H2 blockers and broad-spectrum antibiotics (e.g., 3rd generation cephalosporins or carbapenems) and promotion of breast feeding proved useful. Reduction of early-onset infections (those occurring in the first 3 days of life) can also be obtained by treating maternal vulvo–vaginal candidiasis, which can represent a fastidious problem during pregnancy. In this case, topic azoles (the only recommendable treatment) can represent a kind of “prophylaxis” of early neonatal candidiasis. However, it must always be remembered that prophylaxis reduces the risk of invasive candidiasis but can not completely eliminate its occurrence, with the parallel risk of selecting for antifungal-resistant strains. Clinicians must maintain a high level of suspicion to start an appropriate therapy and strict epidemiological surveillance to identify the occurrence of clusters and the appearance of strains resistant to prophylaxis.