This study aimed to perform a comprehensive systematic review, which reports the role of the Bonar score in the histopathological assessment of tendinopathy and its clinical relevance. To identify all of the studies that reported relevant information on the Bonar scoring system and tendinopathy, an extensive search of the major and the most significant electronic databases (PubMed, Cochrane Central, ScienceDirect, SciELO, Web of Science) was performed. A systematic review of the literature was conducted according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. The extracted data included—year of study, geographical location, type of the study, radiological modifications, gender, number of patients, region of tendinopathy, mean age, control group, characteristics of the Bonar score and alterations in the scale, mean Bonar score, number of investigators, area of tendon investigation, clinical and radiological implications. An extensive search of the databases and other sources yielded a total of 807 articles. Eighteen papers were finally included in this systematic review, and of these, 13 original papers included the clinical and radiological implications of tendinopathy. Radiological evaluation was present in eight studies (both magnetic resonance imaging (MRI) and ultrasound (US)). The clinical implications were more frequent and present in 10 studies. Using the Bonar score, it is easy to quantify the pathological changes in tendinous tissue. However, its connection with clinical and radiological evaluation is much more complicated. Based on the current state of knowledge, we concluded that the neovascularization variable in the Bonar system should be reconsidered. Ideally, the microscopic assessment score should follow the established classification scale with the radiological and clinical agreement and should have a prognostic value.