Driver mutations in lung cancer have been generally considered mutually exclusive; however, multiple gene screenings have recently become mainstream. Therefore, it is not uncommon to identify two or more mutations at first diagnosis, making it difficult to determine which tyrosine kinase inhibitor to administer. A 69-year-old woman complaining of back pain was diagnosed with adenocarcinoma T4N3M1c, stage IVB. Although PCR mutation test detected exon21 L858R point mutation by bronchoscopic sample, the therapeutic effect of afatinib was poor. Subsequently, next-generation sequencing (NGS) panel test of a metastasized bone specimen confirmed BRAF V600E. Furthermore, high sensitivity NGS panel system found the gene mutation allele frequency was higher for BRAF V600E than EGFR exon21 L858R for both primary lung tissue and the metastasized specimen. Subsequent BRAF/MEK inhibitor administration showed a remarkable treatment effect. When two or more driver mutations are detected in lung cancer, confirming the allelic frequency of the mutant gene might be useful in selecting more effective agents for front-line treatment.