Research in dental science reveals a need for enhanced oral healthcare among elite athletes due to the stress generated by excessive exercise. Consideration of the inherent biological distinctions between men and women is crucial in sports dentistry. Thus, this study aims to analyse the differences in oral health status among elite athletes based on gender. A total of 186 elite athletes (150 men and 36 women) recognised in the region of Aragon (Spain) participated in this study (mean age 24.99 ± 9.34), all of whom practise individual sports. Oral health status analysis included: periodontal, malocclusion and tooth status measured using the restoration index (RI) and the decayed, missing and filled teeth (DMFT) index. Women had fewer teeth, a lower restoration index ( < 0.05) and lower DMFT index values ( < 0.001); furthermore, this group showed a greater number of missing teeth ( < 0.001) and decayed teeth ( < 0.05). There were no statistical differences in malocclusion, plaque, gingival bleeding, dental erosion or bruxism values between the genders. Mouthguard usage was low (men = 9.4% vs. women = 14.3%; = 0.57). This study highlights the need for a multidisciplinary approach to address the high prevalence of oral health issues among elite athletes, despite the differences in health status between men and women.