Inulin is a versatile biopolymer that is non-digestible in the upper alimentary tract and acts as a bifidogenic prebiotic which selectively promotes gut health and modulates gut-organ axes through short-chain fatty acids and possibly yet-to-be-known interactions. Inulin usage as a fiber ingredient in food has been approved by the FDA since June 2018 and it is predicted that the universal inulin market demand will skyrocket in the near future because of its novel applications in health and diseases. This comprehensive review outlines the known applications of inulin in various disciplines ranging from medicine to industry, covering its benefits in gut health and diseases, metabolism, drug delivery, therapeutic pharmacology, nutrition, and the prebiotics industry. Furthermore, this review acknowledges the attention of researchers to knowledge gaps regarding the usages of inulin as a key modulator in the gut-organ axes.