Gelam honey (GH) is a prized natural product synthesized from the nectar of flowers from Gelam trees (Melaleuca sp.). Gelam is an evergreen tree species that grows in tropical regions such as Malaysia. GH is a multifloral honey with proven antioxidant and anti-inflammatory properties. However, the beneficial effect of GH on female reproductive tissue has yet to be substantiated. Herein, we investigated the effects of GH administration on the uterine and vaginal epithelial thickness of sexually mature Sprague-Dawley rats. Epithelia thickness could be an indicator of an atrophy manifesting as a symptom of a cardio syndrome. Rats were given oral doses of GH in four groups for 14 days; the lowest dose was 0.2 g GH/kg body weight (bw) rat/day and the highest dose was 8 g GH/kg bw rat/day. The physicochemical characteristics of GH were assessed through hydroxymethylfurfural and moisture content determination and sugar identification. GH attenuated the atrophy of the uterine and vaginal epithelia and increased the thickness of the endometrial stroma and endometrial surface endothelial layer. However, the dissonance observed in the effect of GH administration on the vaginal epithelium requires further investigation. Nevertheless, GH may have a strong potential in attenuating uterine and vaginal atrophies.