Honey is known not only as a natural food but also as complementary medicine. According to the controversial evidence about the effects of honey on blood lipids, this meta-analysis was performed to investigate the potential effects of honey on lipid profiles. Relevant studies were identified by searching PubMed, Web of Science (WOS), Scopus, EMBASE, and Cochrane databases. All human controlled clinical trials (either with a parallel or a crossover design) published in English that reported changes in serum lipid markers (Total Cholesterol (TC), Triglyceride (TG), Low Density Lipoprotein Cholesterol (LDL-C), High Density Lipoprotein Cholesterol (HDL-C), and LDL-C/HDL-C ratio) following honey consumption were considered. Standardized Mean Differences (SMDs) and their respective 95% Confidence Intervals (CIs) were calculated to assess the changes in lipid profiles following honey consumption by random effects model. Statistical heterogeneity, sensitivity analysis, publication bias, and quality of the included studies were assessed, as well. The meta-analysis of 23 trials showed that honey had no significant effects on TC, TG, LDL-C, HDL-C, and LDL-C/HDL-C ratio. Significant heterogeneity was seen among the studies for all the studied factors (I2 index > 50%). Subgroup analysis based on the lipid profile status, types of honey, and intervention duration revealed no significant effect on TC, TG, LDL-C, and HDL-C. Quality of the evidences varied form very low to moderate according to various parameters. In conclusion, honey consumption did not affect serum lipid profiles (TC, TG, LDL-C, HDL-C, and LDL-C/HDL-C ratio).