DNA damage or mutation in cells contributes to tumorigenesis. The transcription factor FOXO1 modulates the expression of genes involved in DNA damage repair, cell cycle arrest and apoptosis. The transcriptional activity of FOXO1 is fundamentally regulated by post-translational modification and subcellular localization. H1299 lung cancer cells were treated with the alkylating agent MNNG, and the cell viability and DNA damage were separately determined by MTT and comet assay. Using immunofluorescence and western blotting, we observed the subcellular localization of FOXO1 and measured the relevant protein expression levels, respectively. To examine cell cycle arrest and apoptosis, flow cytometry analysis was preformed. The interaction between FOXO1 and JNK was analyzed through immunoprecipitation. Our results showed that cell viability was reduced at 24 h after MNNG treatment, and appeared to recover to some degree at 48 h. The increased expression and nuclear export of FOXO1 emerged at 4 h after the treatment. Nuclear FOXO1 played a pivotal role in cell cycle arrest, apoptosis and DNA damage repair by upregulating p27(Kip1), Bim and GADD45 gene expression, respectively. AKT-dependent S256 phosphorylation of FOXO1 and the S473 phosphorylation of AKT were both enhanced following DNA damage. Moreover, our studies revealed that FOXO1 directly interacted with JNK, and the inhibition of the JNK activity led to decreased expression of FOXO1 target genes. These findings suggest for the first time that FOXO1 is a promising candidate substrate for JNK, and the FOXO1-dependent DNA damage repair may be regulated positively by the JNK pathway in H1299 lung cancer cells.