Objective To investigate the role of FAM134B-mediated ER-phagy in the pathogenesis of sepsis. Methods A rat model of sepsis was constructed by Cecal Ligation and Puncture (CLP). The brain expression levels of FAM134B was detected by qRT-PCR and Western Blotting. In LPS induced N2a sepsis cell model, immunofluorescence staining was performed for the distribution of FAM134B in cells. The expression level of autophagy-associated protein LC3, Beclin1 and apoptosis-related protein Caspase-3 were detected by Western blotting. The rate of apoptosis in each group was measured by Annexin V-FITC/PI flow cytometry. Also, the expression levels of autophagy and apoptosis-related proteins were detected in FAM134B over-expression cell lines after LPS treatment. Results The expression of FAM134B in the septic brain were decreased. LPS insulted endoplasmic reticulum autophagy and cell apoptosis were increased. FAM134B overexpression reduced LPS induced damage to cells. Conclusions FAM134B mediated ER-phagy plays a protective role in sepsis.