Fast progress has been witnessed in the field of microfluidic systems and allowed outstanding approaches to portable, disposable, low-cost, and easy-to-operate platforms especially for monitoring health status and point-of-care applications. For this purpose, molecularly imprinted polymer (MIP)-based microfluidics systems can be synthesized using desired templates to create specific and selective cavities for interaction. This technique guarantees a wide range of versatility to imprint diverse sets of biomolecules with different structures, sizes, and physical and chemical features. Owing to their physical and chemical robustness, cost-friendliness, high stability, and reusability, MIP-based microfluidics systems have become very attractive modalities. This review is structured according to the principles of MIPs and microfluidic systems, the integration of MIPs with microfluidic systems, the latest strategies and uses for point-of-care applications and, finally, conclusions and future perspectives.