Recently, some genome-wide association studies have implicated telomerase reverse transcriptase (TERT) and cleft lip and palate transmembrane 1-like gene (CLPTM1L) in lung cancer development. Here, we present a case-control study that evaluates the genetic effects of TERT-rs2736098 and CLPTM1L-rs401681 variants on the risk of lung cancer development in a Chinese male population. We found that the homozygous variant genetic model of the TERT gene was associated with a significantly increased risk of lung cancer with an adjusted odds ratio (OR) of 1.988. The TERT-rs2736098 T allele was also associated with increased lung cancer risk both in adenocarcinoma and squamous cell carcinoma. No association was found between CLPTM1L-rs401681 and lung cancer risk. However, the joint effect of TERT and CLPTM1L variants increased the risk of lung cancer, especially squamous cell carcinoma, with an adjusted OR of 3.274. However, the exact functional effect of these two variant genes remains unclear, and further investigation is needed in the future.