Using resistant lentil cultivars, breeders will be able to control one of the most devastating lentil diseases, Ascochyta blight, effectively. Ascochyta blight caused by the fungus Ascochyta lentis (A. lentis) resulting in over $16 million AUD annual loss in Australia. However, little is known about the genes and molecular mechanisms underlying lentil resistance against A. lentis. To uncover the genetic basis of lentil resistance to A. lentis, differentially expressed genes were profiled in the resistant ‘ILL7537’ and susceptible ‘ILL6002’ lentil genotypes at 2, 6 and 24 hours post inoculation utilizing high throughput RNA-Sequencing. Genotype and time-dependent differential expression analysis identified genes which play key roles in several functions of the defence response comprising fungal elicitors’ recognition and early signalling; structural response; biochemical response; transcription regulators; hypersensitive reaction and cell death; and systemic acquired resistance. Overall, the resistant genotype displayed an earlier and faster detection and signalling response to the A. lentis infection and demonstrated higher expression levels of structural defence-related genes. This study presents a first-time defence-related transcriptome of lentil to A. lentis during the first 24 of pathogen invasion.