The present study aims to explore the glucose-lowering effects of the previously characterised dark tea (Camellia sinensis L.) protein extract (DTPE) from Heimaojian on the spleen–brain axis of diabetic mice. DTPE was orally administrated (50–100 mg/kg) to alloxan-induced mice for 21 d; a biochemical assay and transcriptome profiling (RNA sequencing (RNA-Seq)) were performed. The results showed that DTPE can improve glucose tolerance. Compared with the model group, at day 21, the fasting blood glucose values were significantly (P < 0·05) decreased by 44·9 % (13·8 v. 7·6 mmol/l) and 51·4 % (13·8 v. 6·7 mmol/l) for high dose of DTPE (100 mg/kg) and drug metformin (125 mg/kg) groups, respectively. Subsequently, transcriptome profiling (RNA-Seq) was performed on the spleen and brain of diabetic mice. Totally, fifty-two spleen-derived and forty-seven brain-derived differentially expressed genes related to the synthesis, transport and metabolism of glucose were identified. The regulatory network analysis indicated that DTPE may exert glucose-lowering effects through a thirty-seven-gene sub-network related to metabolism, Parkinson’s disease, oxidative phosphorylation and immunity. In summary, for the first time, the present data revealed that dark tea-derived DTPE could exert a potential anti-hyperglycaemic effect by modulating the spleen–brain axis.