Background: Missing teeth can significantly affect the intercuspal position (ICP) and contribute to temporomandibular joint (TMJ) disorders, which in turn impact the overall masticatory function and oral health. This study investigates the effect of missing teeth on ICP and TMJ symptoms and evaluates the outcomes of prosthodontic rehabilitation. Methods: A total of 120 participants with varying patterns of tooth loss were enrolled in the study, which took place from January to December 2016 in the Department of Prosthodontics at Bangabandhu Sheikh Mujib Medical University and Beau-Dent, Dhaka, Bangladesh. Results: The study included 69 males (57.5%) and 51 females (42.5%) with a mean age range of 36–50 years (40.8%). The results showed that the shift in ICP was most prominent in participants with posterior tooth loss (80%), followed by mixed tooth loss (85.7%) and anterior tooth loss (71.4%). TMJ symptoms were common, with clicking reported by 41.7% of participants, pain by 29.2%, and restricted movement by 16.7%. After prosthodontic rehabilitation, significant improvements were observed in several measures: occlusal contacts increased from 4.5 ± 1.8 to 7.8 ± 2.1 (p < 0.001), bite force improved from 150 ± 30 N to 320 ± 45 N (p < 0.001), and TMJ symptom severity decreased from 3.8 ± 1.2 to 1.2 ± 0.8 (p < 0.001). Conclusion: Missing teeth have a significant impact on intercuspal position and contribute to TMJ symptoms. Prosthodontic rehabilitation effectively restores ICP, improves bite force, and reduces TMJ symptoms.