Background: Endoscopic-ultrasound-guided gastrojejunostomy (EUS-GJ) can be a new alternative for patients with malignant afferent loop syndrome (MALS). However, a fully covered self-expandable metal stent (FCSEMS) has not been well investigated in this setting. Methods: This is a multicenter retrospective cohort study. Consecutive patients that underwent EUS-GJ using a FCSEMS for MALS between April 2017 and November 2022 were enrolled. Primary outcomes were technical and clinical success rates. Secondary outcomes were adverse events, recurrent symptoms, and overall survival. Results: Twelve patients (median age: 67.5 years (interquartile range: 58–74.8); 50% male) were included. The most common primary disease and type of previous surgery were pancreatic cancer (67%) and pancreatoduodenectomy (75%), respectively. Technical success and clinical success were achieved in all patients. Procedure-related adverse events occurred in one patient (8%) with mild peritonitis. During a median follow-up of 96.5 days, one patient (8%) had recurrent symptoms due to the EUS-GJ stent dysfunction; including biliary events unrelated to the EUS-GJ stent, five patients (42%) had recurrent events. The median overall survival was 137 days. Nine patients (75%) died due to disease progression. Conclusions: EUS-GJ with a FCSEMS seems safe and effective for MALS with high technical and clinical success rates and an acceptable recurrence rate.