Covalent organic frameworks (COFs) are an emerging class of crystalline porous polymers with highly tuneable structures and functionalities. COFs have been proposed as ideal materials for applications in the energy-intensive field of molecular separation due to their notable intrinsic features such as low density, exceptional stability, high surface area, and readily adjustable pore size and chemical environment. This review attempts to highlight the key advancements made in the synthesis of COFs for diverse separation applications such as water treatment or the separation of gas mixtures and organic molecules, including chiral and isomeric compounds. Methods proposed for the fabrication of COF-based columns and continuous membranes for practical applications are also discussed in detail. Finally, a perspective regarding the remaining challenges and future directions for COF research in the field of separation has also been presented.