Inflammatory bowel disease (IBD) is chronic inflammatory disorder of the gastrointestinal (GI) tract which pose significant social and economic burden on health system. Crohn’s disease (CD) and ulcerative colitis (UC) are two main classes of IBD which seem to share genetic susceptibly factors at least to some extent. Abnormal immune responses and dysregulation of pre-inflammatory cytokines have been observed in patients with IBD. More recently, several studies have indicated abnormal function and expression levels of a number of non-coding RNAs including both microRNAs (miRNAs) and long non-coding RNAs (lncRNAs). Not surprisingly, dysregulated miRNAs and lncRNAs were mostly enriched in pathways that regulate immune responses such as NF-κB pathway and those influence activity and differentiation of Th17 cells. In the current review, we aim at exploration of the role of miRNAs and lncRNAs in the pathophysiology of IBD. We first summarize the results of studies which reported aberrant expression of these transcripts in colonic tissues or plasma samples of patients with IBD. Then, we discuss the potential of these transcripts as diagnostic markers or therapeutic targets in this regard.