Berberine (BBR) is a widely used anti-diabetic agent, and liver glucokinase (GK) has been reported to be involved. However, the mechanisms of BBR in regulating GK are still unknown. Here, we found that BBR upregulated GK immunofluorescence expression in AML12 cells cultured in high glucose and increased glycogen content simultaneously. BBR improved hyperglycemia in db/db mice, and increased liver glucose-6-phosphate/glucose-1-phosphate (G-6-P/G-1-P) was found by analyzing metabolites (serum, liver, and feces) based on gas chromatography-mass spectrometry (GC-MS) metabolomics. Pharmacokinetics-pharmacodynamics (PK-PD) assessment revealed enriched BBR distribution in the liver, and liver G-6-P had the same trend as the concentration-time curve of BBR. G-6-P is solely catalyzed by GK, and GK activity and expression showed a positive correlation with liver BBR levels. In db/db mice, BBR also upregulated GK in liver fractions (cytoplasm and nucleus) and liver glycogen content. GK functionally worked by dissociating from GK regulatory protein (GKRP), and although GKRP expression was not affected, we found a decreased ratio of GK binding with GKRP in BBR treated db/db mice. In conclusion, our study suggests the dissociation of GK from GKRP as the potential mechanism for liver GK increase upon BBR treatment, which contributes to the anti-diabetic effect of BBR.