Background To investigate the effect of combined oral contraceptives (COC) on orthodontic tooth movement (OTM) and periodontal remodelling in a female rat model. Methods A total of 80 three-month-old female, Sprague-Dawley rats were randomly divided into experimental and control groups. The maxillary first molars were moved mesially using nickel-titanium coil springs (50 g force). The experimental group (N = 40) ingested 1.5 ml COC (Marvelon, 0.12 mg/d, N.V. Organon, Oss, The Netherlands) daily. The control group (N = 40) ingested 1.5 ml saline (0.9% sodium chloride) daily. After 7, 14, 21 and 28 days of force application, 10 rats in each group were euthanased and a vernier calliper was used to measure the orthodontic movement of the first molar. Root resorption at pressure areas was assessed by H and E staining. Micro-CT was used to detect alveolar bone mineral density. Results and conclusion The amount of OTM in the experimental group (0.46 ± 0.16 mm) was significantly less than in the control group (0.85 ± 0.25 mm; p = 0.003) during the 28 days of observation. There were significantly smaller (p = 0.002) root resorption lacunae in the experimental group (111710 ± 4037 pixels) compared with the control group (204962 ± 21318 pixels) after 28 days. There was no statistically significant difference in the bone mineral density between the experimental and control groups throughout the study period (p > 0.05 at each time point). The short-term administration of COC may retard tooth movement and reduce the level of root resorption during OTM in female rats.