This trial assessed the feasibility and acceptability of studying whole systems of TCM and naturopathic medicine (NM) in the treatment of temporomandibular disorders (TMD), and determined whether there is indication to support further research. One hundred and sixty women aged 25–55 years were enrolled in a pilot study using an RCT design of whole system TCM and NM versus state-of-the-art specialty care (SC). The intervention protocols were designed to model the individually tailored type of community care offered in alternative medicine practices using protocols that enhanced similarities among practitioners within each system and permitted full descriptions of the treatments provided. TMD was ascertained using the Research Diagnostic Criteria/TMD; outcomes were self-reported worst and average facial pain and interference with activities (scaled 0–10 where 10 is worst). The patients were randomised to one of three arms; 128 provided endpoint data. TCM and NM demonstrated significantly greater in-treatment reductions for worst facial pain compared to SC (adjusted regression analysis; higher negative values indicate greater improvement, –1.11 ± 0.43, P = 0.010 and –1.02 ± 0.45, for TCM and NM, respectively, compared to SC) and at 3 months post-treatment (–1.07 ± 0.51, and –1.27 ± 0.54, for TCM and NM vs. SC, respectively). Additionally, TCM provided significantly greater decreases in average pain than SC; NM provided significantly greater decreases than SC or TCM in TMD-related psychosocial interference.