Thyroid carcinoma (THCA) is the most universal endocrine malignancy worldwide. Unfortunately, a limited number of large-scale analyses have been performed to identify biomarkers for THCA. Here, we conducted a meta-analysis using 505 THCA patients and 59 normal controls from The Cancer Genome Atlas. After identifying differentially expressed long non-coding RNA (lncRNA) and protein coding genes (PCG), we found vast difference in various lncRNA-PCG co-expressed pairs in THCA. A dysregulation network with scale-free topology was constructed. Four molecules (LA16c-380H5.2, RP11-203J24.8, MLF1 and SDC4) could potentially serve as diagnostic biomarkers of THCA with high sensitivity and specificity. We further represent a diagnostic panel with expression cutoff values. Our results demonstrate the potential application of those four molecules as novel independent biomarkers for THCA diagnosis.