Tobacco-unassociated lung cancer (unLca) is a leading cause of cancer-related death predominantly arising in females and its incidence is increasing. Targeted strategies for unLca treatment and prevention are lacking, and the aetiology of this devastating disease remains poorly understood. Although sex-based differences in unLca incidence are evident, the influence of sex and sex-hormones on lung epithelial cells, their microenvironment, and tobacco-unassociated tumourigenesis, remain largely uncharted. Through extensive analyses of published genomic datasets, we have resolved biologically conserved sex and age-based differences in the transcriptomes of healthy lung cells from never-smokers. Further, interrogation of primary unLca tumours and patient-matched adjacent normal lung tissue transcriptomes reveals sex-specific molecular changes. Finally, a preclinical mouse model of KrasG12D-driven unLca has been dually employed to resolve sex-specific cellular alterations during tumour initiation and progression. These data indicate that sex may shape the mechanisms underpinning unLca development at the molecular level, with implications for the design of targeted, preventative therapies.