Perfluorosulphonic acid-based membranes such as Nafion are widely used in fuel cell applications. However, these membranes have several drawbacks, including high expense, non-eco-friendliness, and low proton conductivity under anhydrous conditions. Biopolymer-based membranes, such as chitosan (CS), cellulose, and carrageenan, are popular. They have been introduced and are being studied as alternative materials for enhancing fuel cell performance, because they are environmentally friendly and economical. Modifications that will enhance the proton conductivity of biopolymer-based membranes have been performed. Ionic liquids, which are good electrolytes, are studied for their potential to improve the ionic conductivity and thermal stability of fuel cell applications. This review summarizes the development and evolution of CS biopolymer-based membranes and ionic liquids in fuel cell applications over the past decade. It also focuses on the improved performances of fuel cell applications using biopolymer-based membranes and ionic liquids as promising clean energy.