(1) Background: The aim of this study was to investigate the agreement between a clinical diagnosis based on research diagnostic criteria/temporomandibular disorders (RDC/TMD) and high-field magnetic resonance imaging (MRI) findings of temporomandibular joints (TMJs) in asymptomatic females. (2) Methods: A prospective study on 100 females (200 TMJs) was performed, using clinical examinations (RDC/TMD) and same-day MRIs of TMJs on a 3T MR unit. The inclusion criteria were as follows: females, age > 18, the presence of upper and lower incisors, and an understanding of the Serbian language. Descriptive statistics (means and standard deviations) and ANOVA with a post hoc Tukey test for differences among the patient subgroups was performed. The agreement between the clinical and MRI findings was determined using Cohen’s kappa coefficient (k < 0.21 slight, 0.21–0.4 fair, 0.41–0.6 moderate, 0.61–0.8 substantial, and 0.81–1 almost perfect). The statistical significance was set atp≤ 0.05. (3) Results: Normal findings were observed in 86.7%, disc dislocation (DD) was observed in 9.2%, and arthralgia/osteoarthritis/osteoarthrosis was observed in 2.6% of TMJs using RDC/TMD. On the MRI, normal findings were observed in 50.5%, disc dislocation was observed in 16.3%, and arthralgia/osteoarthritis/osteoarthrosis was observed in 23.5% of TMJs. The anterior DD with reduction showed fair agreement of the clinical and MRI findings (k = 0.240,p< 0.001) compared with the DD without reduction (k = 0.355,p< 0.001). Both showed high specificity (94.9% and 99.4%) but low sensitivity (24.2% and 25.0%). The sensitivity in osteoarthritic changes was low (4.8%), but the specificity remained high (96.2%). (4) Conclusions: The sensitivity of the clinical examination remains low compared with 3T MRI, especially in osteoarthritic changes and anterior DD with reduction. However, the number of false positive diagnoses using RDC/TMD is low in asymptomatic patients. RDC/TMD remains a sensible method for establishing a clinical diagnosis and avoiding the overtreatment of asymptomatic patients.