Chronic obstructive pulmonary disease (COPD) and idiopathic pulmonary fibrosis (IPF) are two pathologically distinct chronic lung diseases that are associated with cigarette smoking. Genetic studies have identified shared loci for COPD and IPF, including several loci with opposite directions of effect. The existence of additional shared genetic loci, as well as potential shared pathobiological mechanisms between the two diseases at the molecular level, remains to be explored. Taking a network-based approach, we built disease modules for COPD and IPF using genome-wide association studies-implicated genes. The two disease modules displayed strong disease signals in an independent gene expression data set of COPD and IPF lung tissue and showed statistically significant overlap and network proximity, sharing 19 genes, including ARHGAP12 and BCHE. To uncover pathways at the intersection of COPD and IPF, we developed a metric, NetPathScore, which prioritizes the pathways of a disease by their network overlap with another disease. Applying NetPathScore to the COPD and IPF disease modules enabled the determination of concordant and discordant pathways between these diseases. Concordant pathways between COPD and IPF included extracellular matrix remodeling, Mitogen-activated protein kinase (MAPK) signaling and ALK pathways, whereas discordant pathways included advanced glycosylation end product receptor signaling and telomere maintenance and extension pathways. Overall, our findings reveal shared molecular interaction regions between COPD and IPF and shed light on the congruent and incongruent biological processes lying at the intersection of these two complex diseases.