Previously, we showed that oral administration of probiotics, Lactobacillus acidophilus NS1 (LNS1), improved insulin sensitivity in high-fat-diet-fed mice (HFD mice). Furthermore, LNS1-conditioned media (LNS1-CM) reduced HNF4α transcription activity and the expression of phosphoenol pyruvate carboxykinase (PEPCK), a key enzyme in gluconeogenesis in HepG2 cells. In this study, we demonstrated that LNS1 administration increased the expression of glycosyltransferase 2 (GYS2) and glucose transporter 2 (GLUT2), while reduced the expression of glucose-6-phosphatase (G6PC) expression in liver of HFD mice. Furthermore, LNS1 suppressed hepatic expression of glucokinase regulatory unit (GCKR) in HFD mice without changing the mRNA levels of glucokinase (GCK), suggesting that LNS1 may inhibit nuclear GCK activity. Consistently, addition of LNS1-CM to HepG2 cells increased the mRNA levels of GYS2 and GLUT2 with reduced mRNA levels of G6PC and GCKR. Moreover, hepatic glycogen contents were increased in HFD mice upon administration of LNS1. Together, these results suggest that LNS1 facilitates glycogen accumulation in liver by regulating the expression of genes involved in glycogen metabolism, contributing to improved insulin sensitivity in the HFD mice.