The decision of the appropriate treatment for pancreatic cystic lesions (PCLs) is becoming increasingly important as the number of incidentally found PCLs increases. A range of modalities have been attempted because there has been an increasing demand for minimally invasive treatment for PCLs due to the large burden of a surgical resection. Endoscopic treatment using endoscopic ultrasonography (EUS), a representative of minimally invasive therapy, can be categorized into two types: ablation therapy by the injection of drugs and topical thermal coagulative therapy through the high topical energy. A number of studies reported the feasibility and efficacy of these treatments; the most common is EUS-guided ablation for PCLS with ethanol alone or in combination with anticancer drugs. Although ablation therapies with drug injection have proven safety and feasibility, there is no consensus regarding the actual treatment effects and indications of these modalities. EUS-guided radiofrequency ablation was recently attempted as a representative method of local thermal coagulation, but further studies will be needed because of the lack of evidence of its feasibility and safety. In addition, a range of treatments for malignant tumors rather than PCLs have been attempted, such as EUS-guided photodynamic therapy, EUS-guided neodymium-doped yttrium aluminum garnet laser, and high-intensity focused ultrasound, based on the data from animal experiments. Through further study, endoscopic treatment is expected to become established as a useful treatment modality for PCLs.