The appearance of biological molecules, so-called biomarkers in body fluids at abnormal concentrations, is considered a good tool for detecting disease. Biomarkers are usually looked for in the most common body fluids, such as blood, nasopharyngeal fluids, urine, tears, sweat, etc. Even with significant advances in diagnostic technology, many patients with suspected infections receive empiric antimicrobial therapy rather than appropriate treatment, which is driven by rapid identification of the infectious agent, leading to increased antimicrobial resistance. To positively impact healthcare, new tests are needed that are pathogen-specific, easy to use, and produce results quickly. Molecularly imprinted polymer (MIP)-based biosensors can achieve these general goals and have enormous potential for disease detection. This article aimed to overview recent articles dedicated to electrochemical sensors modified with MIP to detect protein-based biomarkers of certain infectious diseases in human beings, particularly the biomarkers of infectious diseases, such as HIV-1, COVID-19, Dengue virus, and others. Some biomarkers, such as C-reactive protein (CRP) found in blood tests, are not specific for a particular disease but are used to identify any inflammation process in the body and are also under consideration in this review. Other biomarkers are specific to a particular disease, e.g., SARS-CoV-2-S spike glycoprotein. This article analyzes the development of electrochemical sensors using molecular imprinting technology and the used materials’ influence. The research methods, the application of different electrodes, the influence of the polymers, and the established detection limits are reviewed and compared.