Inflammatory Bowel Disease (IBD) affects a substantial global population and is characterized by chronic inflammation primarily in the gastrointestinal tract. The pathophysiology of IBD is intricate and involves a combination of genetic, environmental, and immune-related factors. This article aims to discuss the current understanding of IBD pathophysiology, focusing on the roles of genetics, environmental triggers, and the immune system in disease development and progression. In addition, the review covers the existing treatment options for IBD, including medical and surgical interventions while addressing the challenges associated with managing this chronic condition. Furthermore, the article explores the utility of disease modeling techniques, such as animal models, in vitro organoid models, and microfluidic organ-on-a-chip devices, for studying IBD pathophysiology and evaluating potential therapeutic interventions. It is important to note that conventional two-dimensional (2D) cell cultures are limited in capturing essential physical and biochemical cues, despite displaying lineage-specific differences. The translation of data from animal models to human physiology in major systems undermines the reliability of the generated data. To address these limitations, one noteworthy solution is the utilization of microfluidic-based organ-on-a-chip devices, which can effectively mimic organ functionality. These devices are developed based on principles of microfluidics, materials science, and cell biology. Overall, this comprehensive review provides insights into the pathophysiology of IBD, current treatment options, and disease modeling approaches, including emerging technologies, such as organoids and organ-on-a-chip. These advancements offer promising avenues for enhancing our understanding of IBD and developing more efficient therapies for this debilitating condition.