Recently, long non-coding RNAs (lncRNAs) have been shown to play critical roles in lung adenocarcinoma (LUAD). The present study aimed to explore the effect of LINC00982 and PRDM16 on clinical features and survival in LUAD. We found that LUAD patients demonstrated lower expression and copy number variation but higher methylation of long intergenic non-protein coding RNA 982 (LINC00982) and PR domain containing 16 (PRDM16) compared with controls. Thus, we divided the LUAD patients into two groups according to the median expression of LINC00982 and PRDM16. Through differential expression, KEGG pathway enrichment and Ingenuity (R) Pathway Analysis (IPA), we found that patients with low expression of both LINC00982 and PRDM16 presented with more deregulated genes, as well as more significant pathways, than patients with high expression of these two genes. In addition, Kaplan-Meier curves and Cox proportional hazards models revealed that patients with low expression of LINC00982, PRDM16 or both, showed poorer survival than the groups with high expression of LINC00982, PRDM16. We further used multivariate survival models to verify these results. Furthermore, we confirmed that the expression of LINC00982 and PRDM16 was significantly decreased in LUAD cell lines compared to normal cell lines in vitro. In conclusion, the present study revealed that LINC00982 and PRDM16 may serve as biomarkers or potential drug targets for the diagnosis and therapy of LUAD.