Background: Tuberous sclerosis complex (TSC) is a rare genetic disorder with neurological and systemic involvement. The relationship of TSC and the anti-seizure medications (ASM) and mammalian target of rapamycin (mTOR) inhibitors used in its treatment with oral and dental health is not fully understood. This study compared oral and dental health parameters in children with TSC and healthy controls and investigated the association between pharmacological treatment exposure and these parameters. Methods: A case-control study was conducted between January and November 2025 at the Istanbul University Faculty of Medicine Pediatric Neurology Clinic on 19 children aged 3–18 years with TSC and 19 age and sex matched healthy controls. Gingival index, gingival overgrowth index, fibroma, enamel pits, decayed/filled/missing teeth (dmft/DMFT) scores, toothbrushing frequency, dental visit frequency, and Wong-Baker pain scores were evaluated. In the TSC group, disease duration, comorbid conditions, and duration of ASM and mTOR inhibitor use were also recorded. Matched between-group comparisons were performed using paired statistical tests, and associations were assessed using Spearman correlation analysis. Results: Gingival index, gingival overgrowth, and enamel pits were significantly higher in the TSC group than in controls (p < 0.05). No significant differences were found between in toothbrushing frequency, dental visits, or fibroma group. Within the TSC group, longer ASM exposure was positively correlated with gingival index and gingival overgrowth, whereas mTOR inhibitor exposure showed a moderate positive correlation with gingival overgrowth but no significant correlation with gingival index. Conclusions: Compared with age and sex matched controls, children with TSC showed higher gingival index scores (2.0 vs. 1.0), greater gingival overgrowth (1.0 vs. 0.0), and a higher prevalence of enamel pits (57.9% vs. 15.8%). Longer ASM exposure was strongly correlated with gingival index (ρ = 0.735) and gingival overgrowth (ρ = 0.801), whereas mTOR inhibitor exposure was moderately correlated only with gingival overgrowth (ρ = 0.488).