ABSTRACT Objective Temporomandibular disorders (TMDs) are heterogeneous conditions of unclear aetiology involving the temporomandibular joint, masticatory muscles and neural tissues. Limited understanding of their pathogenesis hampers accurate diagnosis and targeted treatment. Therefore, this study aimed to identify salivary microRNA (miRNA) signatures associated with TMDs to support future diagnostic, therapeutic and prognostic applications. Materials and Methods Unstimulated cell‐free saliva (5 mL) was collected from 9 adult female TMD subjects (using Diagnostic Criteria/TMD) and eight healthy female controls of similar ages. Total RNA was extracted, small RNA libraries were prepared, and sequencing was performed using Illumina NovaSeq 6000. Reads were aligned to the human genome (GRCh38) via STAR. Differential expression analysis was conducted using DESeq2, followed by functional enrichment via miEAA 2.1. Results A total of 187 salivary miRNAs were significantly differentially expressed between TMD and control groups (adjusted p < 0.05; log2‐fold change > +1 or < −1), with 125 upregulated and 62 downregulated in TMD subjects. Several differentially expressed miRNAs were linked to the negative regulation of cadherin‐mediated cell–cell adhesion, neurogenesis and chemokine production. Some overlapped with miRNAs implicated in rheumatoid arthritis and osteoarthritis, suggesting shared mechanisms. While no clear association was found between miRNA and TMD phenotypes, 5 miRNAs were strongly ( R = 0.67–0.77) and significantly ( p < 0.05) correlated with pain intensity and chronic pain grade. Conclusions Salivary miRNA profiling offers promise as a non‐invasive diagnostic tool for TMDs, with the potential to uncover molecular endotypes and disease mechanisms not evident through clinical evaluation. Future studies with larger, more diverse cohorts are needed to validate these findings and assess their clinical utility.