Objectives: Temporomandibular disorders (TMDs) are common but often underrecognized and inadequately managed in primary healthcare, which may delay diagnosis and appropriate care. This study aimed to compare TMD-related knowledge, awareness, and clinical practices between dentists and physicians working in primary care and to identify factors associated with higher diagnostic confidence. Methods: A cross-sectional survey was conducted among dentists and physicians working in Croatian primary healthcare. TMD-related knowledge, clinical confidence, screening practices, and referral patterns were assessed using a structured questionnaire. Results: Dentists demonstrated significantly higher overall knowledge scores than physicians (15.6 ± 1.7 vs. 13.2 ± 4.1; p < 0.001), as well as greater diagnostic and therapeutic confidence (all p < 0.001). Routine TMD screening was reported by only 21.8% of participants, more frequently by dentists than physicians (36.1% vs. 8.2%; p < 0.001). Most respondents preferred referral rather than independent management. Regression analysis identified profession as the only independent predictor of higher TMD-related knowledge (p = 0.003). Insufficient knowledge, experience, and lack of confidence were the most reported barriers, particularly among physicians. Conclusions: The findings indicate clinically relevant gaps in TMD preparedness within primary healthcare, especially among physicians, despite frequent patient contact. Strengthening undergraduate and continuing education, promoting interdisciplinary training, and establishing clearer referral pathways may enhance early recognition and improve primary-level management of TMD.