Atrial fibrillation (AF) is the most common arrhythmia in patients with hypertrophic cardiomyopathy (HCM). The present study aimed to investigate the incidence and prognostic impact of newly detected AF after cardiac implantable electronic device (CIED) implantation with HCM patients. Fifty-six patients (33 men, age 57 ± 17 years) with HCM who underwent CIED implantations with no previous history of AF at the time of implantation (ICD n = 46, Pacemaker n = 10) were retrospectively enrolled. During 5.7 ± 3.6 years of follow-up, AF was newly detected in 20 (36%) of 56 patients after the CIED implantation (AF group) and the rest of the patients had no newly detected AF (non-AF group). The presence of mitral regurgitation (HR 8.49; 95% CI 2.29-30.6 P < 0.01) and concomitant NYHA II-IV (HR 3.37; 95% CI 1.30-8.86 P = 0.01) were the independent predictors of newly detected AF. During the follow-up, all patients in the AF group started anticoagulation mean 21 days after detection of AF, and none had a stroke during the follow-up period. The rate of appropriate ICD therapy (log-rank P = 0.95), inappropriate ICD therapy (log-rank P = 0.78), and all-cause death (log-rank P = 0.23) were similar between the two groups. However, the incidence of hospitalizations due to heart failure was higher in the AF group (55% vs. 6% log-rank P < 0.01). In conclusion, the incidence of newly detected AF after CIED implantations in HCM patients was high. The newly detected AF was associated with worsening heart failure and careful follow-up is recommended.