Introduction: Over the past decade, Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF MS) has transitioned from a promising novelty to an indispensable tool in clinical microbiology. This review examines the successes, limitations, and profound clinical impact of MALDI-TOF MS in the identification of fungal pathogens since its widespread adoption. Methods: A comprehensive review of the literature was conducted to synthesize the progress of MALDI-TOF MS in mycology over the last ten years. The focus was placed on its application to filamentous fungi and rare yeasts, its current limitations, and its documented effects on patient management. Results: MALDI-TOF MS has achieved remarkable success in the rapid and accurate identification of common and rare yeast species, with identification times reduced from days to minutes. Its application to filamentous fungi (molds) has been more challenging but has matured significantly through improved sample preparation protocols and expanded spectral databases. The technology has proven to be a powerful tool for identifying clinically relevant molds like Aspergillus, Fusarium, and Mucorales. However, limitations persist, including incomplete databases for rare or newly described species, difficulties in distinguishing closely related (cryptic) species, and the lack of standardized protocols for mold extraction. Conclusion: MALDI-TOF MS has fundamentally transformed the workflow of the clinical mycology laboratory. It is a robust, rapid, and cost-effective identification method that has overcome many of the limitations of traditional techniques. While ongoing efforts are needed to expand spectral databases and standardize protocols, its role in improving the diagnosis and management of invasive fungal infections is firmly established.