Due to their advantages of good flexibility, low cost, simple operations, and small equipment size, electrochemical sensors have been commonly employed in food safety. However, when they are applied to detect various food or drug samples, their stability and specificity can be greatly influenced by the complex matrix. By combining electrochemical sensors with molecular imprinting techniques (MIT), they will be endowed with new functions of specific recognition and separation, which make them powerful tools in analytical fields. MIT-based electrochemical sensors (MIECs) require preparing or modifying molecularly imprinted polymers (MIPs) on the electrode surface. In this review, we explored different MIECs regarding the design, working principle and functions. Additionally, the applications of MIECs in food and drug safety were discussed, as well as the challenges and prospects for developing new electrochemical methods. The strengths and weaknesses of MIECs including low stability and electrode fouling are discussed to indicate the research direction for future electrochemical sensors.