Pancreatic cystic lesions (PCLs) have increased in prevalence due to the increased usage and advancements in cross-sectional abdominal imaging. Current diagnostic techniques cannot distinguish between PCLs requiring surgery, close surveillance, or expectant management. This has increased the morbidity and healthcare costs from inappropriately aggressive and conservative management strategies. Endoscopic ultrasound (EUS) needle-based confocal laser endomicroscopy (nCLE) allows for microscopic examination and delineation of the surface epithelium of PCLs. Landmark studies have identified characteristics distinguishing various types of PCLs, confirmed the high diagnostic yield of EUS-nCLE (especially for PCLs with an equivocal diagnosis), and shown that EUS-nCLE helps to change management and reduce healthcare costs. Refining procedure technique and reducing procedure length have improved the safety of EUS-nCLE. The utilization of artificial intelligence and its combination with other EUS-based advanced diagnostic techniques would further improve the results of EUS-based PCL diagnosis. A structured training program and device improvements to allow more complete mapping of the pancreas cyst epithelium will be crucial for the widespread adoption of this promising technology.