Background: This study investigated the factors involving joint effusion in patients with temporomandibular disorders. Methods: The magnetic resonance images of 131 temporomandibular joints (TMJs) of patients with temporomandibular disorders were evaluated. Gender, age, disease classification, duration of manifestation, muscle pain, TMJ pain, jaw opening disturbance, disc displacement with and without reduction, deformation of the articular disc, deformation of bone, and joint effusion were investigated. Differences in the appearance of symptoms and observations were evaluated using cross-tabulation. The differences in the amounts of synovial fluid in joint effusion vs. duration of manifestation were analyzed using the Kruskal–Wallis test. Multiple logistic regression analysis was performed to analyze the factors contributing to joint effusion. Results: Manifestation duration was significantly longer when joint effusion was not recognized (p< 0.05). Arthralgia and deformation of the articular disc were related to a high risk of joint effusion (p< 0.05). Conclusions: The results of this study suggest that joint effusion recognized in magnetic resonance imaging was easily observed when the manifestation duration was short, and arthralgia and deformation of the articular disc were related to a higher risk of joint effusion.