Introduction The effect of honey consumption in diabetic patients has been contradictory. The aim of the present animal study was to compare the effect of different types of honey on the lipid profile in diabetic rats. Material and methods Sixty-four male Wistar rats were divided into two main groups: a streptozotocin-induced diabetes mellitus (DM) group (including four subgroups) and a healthy group (including four subgroups), based on random allocation. Three subgroups of each main group were given 1 mg/kg of three different types of honey (acacia, astragalus, and artificial honey) by oral gavage for 10 weeks. The control groups were given distilled water. Blood samples were collected, and the lipid profile was measured and compared between the eight groups after the intervention. Results The levels of LDL, triglycerides (TG), and total cholesterol (Tchol) in DM rats treated with astragalus honey were significantly lower and the HDL level was significantly higher compared to the other DM and healthy groups (all p -values < 0.05). LDL, TG, and Tchol levels in DM rats treated with artificial honey were significantly higher, and HDL levels were significantly lower than for other types of honey and for the control groups (all p -values < 0.05). LDL, HDL, TG, and Tchol levels in healthy rats were not significantly different between the groups ( p -value > 0.05). Conclusions Different types of honey (acacia, astragalus, and artificial honey) had various effects on serum lipid profiles in diabetic rats. The results of this study indicated that the effect of honey on diabetic patients can vary widely based on its source.