Background: The visibility of Rare Diseases is a new challenge for society. These diseases are numerous, heterogeneous in nature and distribution, characterized by a high mortality rate but low prevalence, and usually presenting a severe evolution. Adherence to medication studies in rare diseases are uncommon, due to treatment scarcity. Objectives: The main purpose of this study is to do a meta-analysis, evaluating the level of adherence to medication in the most prevalent rare diseases. Methods: This work is a systematic review, and meta-analysis was registered in the International Prospective Register of Systematic Reviews (PROSPERO) (Registration number: CRD42022372843) and conducted according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) statement. Adherence to treatment in this systematic review and meta-analysis was collected from all studies included, based on the crude numerators and denominators reported, using either the Morisky Medication Adherence Scale 4 or -8. Results: A total of 54 records were identified through database searches, or after screening relevant manuscripts’ references. Finally, 18 studies were included in this systematic review and meta-analysis. A total of 1559 participants (54.18% women) aged less than 84 years old were included. Twelve studies used the MMAS-8. In 8 of them, they established the level of adherence to treatment in three categories (low, medium, and high), with the mean prevalence in each of them being 41.4%, 30.4%, and 28.2%, respectively. Conclusions: The results observed in adherence to treatment in patients with rare diseases show great variability, due to the different aspects involved in the greater or lesser applicability of the medication.