Background: Isolated manual therapy techniques (MT) have shown beneficial effects in patients with temporomandibular disorders (TMD) but the effect of the combination of such techniques, together with the well-stablished splint therapy (ST) remains to be elucidated. Objective: This study was conducted to ascertain whether a combined program of MT techniques, including intraoral treatment, plus traditional ST improves pain and clinical dysfunction in subjects with TMD. Methods: A preliminary trial was conducted. 16 participants were assigned to either the MT plus ST-Experimental Group (EG, n = 8) or the ST alone—Control Group (CG, n = 8). Forty-five minute sessions of combined MT techniques were performed, once a week for four weeks. Three evaluations were conducted: baseline, post-treatment, and one-month follow-up. Outcome measures were pain perception, pain pressure threshold (PPT), TMD dysfunction, and perception of change after treatment. Results: EG showed significant reduction on pain, higher PPT, significant improvement of dysfunction and significantly positive perception of change after treatment (p < 0.05 all). Additionally, such positive effects were maintained at follow-up with a high treatment effect (R2 explaining 26.6–33.2% of all variables). Conclusion: MT plus ST showed reduction on perceived pain (3 points decrease), higher PPT (of at least 1.0 kg/cm2), improvement of disability caused by pain (4.4 points decrease), and positive perception of change (EG: 50% felt “much improvement”), compared to ST alone.