The aim of this study was to evaluate the effects of coenzyme Q10 in the treatment of endometriosis rat models. Twenty seven Sprague Dawley rats were divided into four groups; Control Group (n = 7; Endometriosis group), Reference Group (n = 6; Endometriosis + Buserelin acetate, 20 mg/kg), CoQ10 Group-I (n = 7; Endometriosis + CoQ10, 50 mg/kg) and CoQ10 Group-II (n = 7; Endometriosis + CoQ10, 100 mg/kg). At the end of the experiment, all the rats were sacrificed, and the volume and histoarchitecture of endometrial implants were evaluated. The mast cells were determined by Toluidine blue and collagen fiber density was analysed by Masson's Trichrome staining. Tumour necrosis factor and vascular endothelial growth factor (VEGF) levels were analysed by enzyme-linked immunosorbent assay in peritoneal fluid and VEGF and matrix metalloproteinase-9 (MMP-9) were evaluated by immunohistochemistry. Terminal deoxynucleotidil transferase-mediated dUTP Nick end labelling (TUNEL) was also used for the detection of apoptotic cells. The CoQ10 treatment significantly decreased the volume of endometriotic implants, VEGF, and MMP-9 immunoreactivity and increased TUNEL-positive cells. The findings of the study suggest that CoQ10 can be used in endometriosis treatment by suppressing the endometriotic implants.IMPACT STATEMENT What is already known on this subject? Endometriosis is a gynaecological disorder and previous studies have shown that different treatments with antioxidants cause significant regression in the endometriotic implants. What the results of this study add? In this study, CoQ10 reduced intra-abdominal adhesion scores and volume of the endometriotic implants. In addition, CoQ10 treatment affected mast cell, TNF-alpha, VEGF, and MMP-9. What of these findings for clinical practice and/or further research? CoQ10 treatments may be possible to apply, it can contribute to science in terms of a new therapeutic treatment for endometriosis. Further studies are required to evaluate the Coenzyme Q10's effects on pain and subfertility in endometriosis.