Aims and background: Accurate identification of Candida species and their antifungal susceptibility (AFS) profiles, especially in neonates, is important in the era of emerging pathogens like Candida and the growing resistance to commonly used antifungal agents. This study aimed to accurately identify Candida species using automated identification systems, specifically matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS). Additionally, we assessed the AFS patterns of these isolates using the automated VITEK 2 Compact system. Materials and methods: This prospective study was conducted in the Department of Microbiology at SMS Medical College, Jaipur, Rajasthan, from April 2023 to August 2023. Blood culture samples were processed using the automated BacT/Alert system, followed by Gram staining and inoculation onto blood agar and MacConkey agar. Gram results were communicated to the clinicians on the same day. Smears showing budding yeast cells were further analyzed using MALDI-TOF MS for species identification, and their minimal inhibitory concentrations (MICs) were determined using the VITEK 2 Compact system. Results: Among 161 Candida isolates, Candida krusei emerged as the most prevalent species (35%), followed by C. tropicalis (20%) and C. glabrata (15%). Male children constituted 69% of the total cases. Voriconazole demonstrated the highest sensitivity (86%), followed by micafungin (84%), caspofungin (79%), and amphotericin B (78%). Conversely, 5-flucytosine exhibited the lowest susceptibility (35%), along with fluconazole (49%). Conclusion: Identification of yeasts from blood culture by automated systems like MALDI-TOF and VITEK 2 is a fast, reliable technique, offering clinicians timely and precise information crucial for prompt patient management and targeted treatment strategies. Clinical significance: C. krusei has emerged as the most prevalent species in neonates amid the increasing trend of C. tropicalis over the past few years. We have adopted technologies like MALDI-TOF MS and VITEK 2 systems for prompt identification of Candida species, thereby speeding up the diagnosis and providing early reports to clinicians, ultimately saving the lives of neonates.