Background: Temporomandibular disorders (TMDs) are multifactorial conditions affecting the masticatory muscles and temporomandibular joints, often exacerbated by psychosocial stressors such as academic pressure in adolescents. Emerging evidence suggests that magnesium plays a critical physiological role in neuromuscular regulation and stress modulation, but its therapeutic efficacy in TMD management remains underexplored. Methods: A clinical study was conducted involving 100 adolescents diagnosed with TMDs, divided into two equal groups (n = 50 each). Group A received a conventional treatment comprising NSAIDs and muscle relaxants, along with a physiology-based magnesium supplementation regimen (400 mg elemental magnesium daily for 30 days), while Group B received only the conventional treatment. Baseline and post-treatment assessments included serum magnesium levels, Visual Analogue Scale (VAS) for pain, and academic stress scores. Data were analysed using paired and independent t-tests, Pearson correlation, and confidence intervals to compare intra- and inter-group changes. Results: Group A showed a significant reduction in academic stress (from 27.81 ± 3.48 to 24.15 ± 3.62, p = 0.046), accompanied by a substantial reduction in pain intensity (VAS score from 6.42 ± 0.98 to 2.44 ± 0.85, p < 0.001) and increase in serum magnesium levels (from 0.673 ± 0.028 to 0.744 ± 0.035 mmol/L) compared to Group B. Group B had a modest decrease in pain (to 4.36 ± 0.79) with no significant change in magnesium. These findings reinforce the hypothesis that as magnesium levels increase, academic stress decreases, thereby contributing to a reduction in TMD-related pain. Conclusion: Magnesium supplementation was more effective when combined with conventional treatment than conventional therapy alone in reducing TMD pain and improving magnesium levels. These findings suggest that academic stress and magnesium deficiency together may improve TMD management in adolescents.