Introduction Pulmonary fibrosis is a rare disease characterised by scarring of the lung where lung transplant remains the only effective cure. Type II alveolar epithelial (AT2) cells play a key role in the fibrotic process. AT2 cells generated from patient-derived induced pluripotent stem cells (iAT2) carrying a mutation in SFTPC have recently been employed as a novel disease modelling platform. Non-coding RNAs (ncRNAs) are thought to be involved in disease pathogenesis but little is known about their precise role. We hypothesize that ncRNAs such as microRNAs (miRNAs) and circular RNAs (circRNAs) contribute to AT2 injury. Aim Here we aim to assess the expression and function of ncRNAs in the iAT2 model and clinical samples with the ultimate goal to explore their therapeutic potential in pulmonary fibrosis. Methods MiRNA and circRNA expression was measured in iAT2s carrying the SFPTC mutation vs CRISPR-Cas9 corrected clone using Arraystar Human Small RNA and CircRNA Microarray, respectively. Differentially expressed ncRNAs with fold changes ?1.5 and p<0.05 between the two groups were identified using Volcano Plot filtering. Results A total of 2560 miRNAs and 13548 circRNAs were detectable in the iAT2 model. 131 miRNAs and 905 circRNAs were significantly upregulated in SFPTC-mutant compared to corrected iAT2s, while 97 and 684 were downregulated, respectively. Conclusions NcRNAs are heavily dysregulated in SFPTC-mutant vs corrected iAT2s. Pathway analysis followed by qRT-PCR validation in clinical samples and functional studies in the iAT2 cell model will be carried out to clarify their biological role in AT2 injury.