Background: Use of minimally invasive techniques has reduced mortality in walled-off pancreatic necrosis (WON) but may be costly. The aim of this study was to evaluate the actual costs associated with the endoscopic management of patients with WON. Methods: We included a retrospective cohort of WON patients treated with endoscopic, transgastric drainage and necrosectomy (ETDN) during 2013–2014. Costs were calculated for six sub-areas based on a micro-costing model. Students T-test and non-parametric analysis of variance were performed to evaluate costs in relation to disease etiology and outcome. Results: We included 58 patients (50% men, median age 57 years). The most common etiologies were gallstones (57%) and alcohol (19%). Nine patients (16%) died during admission. The median length of stay was 50 days (IQR 31 days). Eighteen patients (31%) needed treatment in our intensive care unit with a median length of stay of 16 days (IQR 31 days). The mean costs and standard deviation of costs (SD) per patient were: diagnostic imaging $2,431 ($2,301), laboratory tests $3,579 ($2,477), blood products $982 ($1,734), endoscopic treatment $3,794 ($1,777), medicine $5,440 ($6,656), and ward cost $41,260 ($35,854). The mean total cost was $57,486 ($46,739). Post-ERCP pancreatitis and mortality predicted higher costs. Conclusions: This study sheds light on the different costs associated with endoscopic treatment of WON. As nearly three quarters of the costs are related to ward care, initiatives aimed at reducing the length of hospital stay may have a great impact on making endoscopic treatment more cost effective.