Atrial fibrillation (AF) and hypertrophic cardiomyopathy (HCM) are two very common clinical entities, which often occur simultaneously, giving a hard time to both patients and cardiologists. Myocyte hypertrophy, myocyte disarray and interstitial fibrosis in the left atrium (LA) predisposes to atrial arrhythmias due to modifications of the substrate that promote re-entry. AF is usually poorly tolerated due to the shortening of the diastolic time with rapid heart rates and the lack of the atrial contribution to the diastolic filling in patients who often have a previous diastolic dysfunction. AF onset frequently results in exercise intolerance and recurrent heart failure admissions and also has prognostic implications. Early maintenance of sinus rhythm appears as a worthy approach in these patients, especially when started early in the course of the disease. However, treatment with antiarrhythmic (AA) agents in HCM patients is less effective than in patients without the disease, and concerns regarding safety frequently limit the long-term adherence. Catheter ablation has limited efficacy in patients with persistent AF but can play an important role in patients with paroxysmal AF, emphasizing the importance of an accurate patient selection. The aim of this review is to provide an overview of the pathophysiology of combined HCM and AF and the principal pharmacological and non-pharmacological treatments recommended in this complex clinical scenario.