Background Laparoscopic transgastric necrosectomy (LTGN) has been used in treatment of walled-off pancreatic necrosis (WON) for more than a decade. However, the safety and effectiveness of LTGN for WON with sinistral portal hypertension was still unclear. Methods WON patients with sinistral portal hypertension treated in our department between January 2011 and December 2018 were included and retrospectively analyzed in this study. Patients were divided into two groups according to different surgical approaches, LTNG or laparoscopic assisted trans-lesser sac necrosectomy (LATLSN). Perioperative and long-term outcomes were compared between two groups. Results 312 cases diagnosed with WON were screened and 53 were finally included in this study. Of the included patients, 21 and 32 cases were received LTGN and LATLSN, respectively. LTGN was associated with significantly lower morbidity than LATLSN (19.0% vs 46.9%, p = 0.04) and similar severe complication (Clavien-Dindo >= III) rate (12.5% vs 19.0%, p = 0.70). LTGN did not increase the rate of postoperative hemorrhage (9.5% vs 6.3%, p = 1.00) and mortality (9.5% vs 9.4%, p = 1.00). After 39 (11-108) months follow-up, the recurrence rate of WON and long-term complications were also comparable between groups. Conclusion From current data, LTGN was safe and effective in treatment of WON patients with sinistral portal hypertension in terms of short- and long-term outcomes.