Several trials demonstrated that frequent right ventricular apical pacing (RVAP) was associated with cardiac dysfunction and an increased rate of heart failure hospitalization. However, there are few reports about the 12-lead electrocardiogram (12-ECG) parameters at the time of device implantation to predict deterioration of LVEF in patients with frequent RVAP. We retrospectively studied 115 consecutive patients undergoing pacemaker or implantable cardioverter-defibrillator implantation with RVAP, with rate of ventricular pacing ≥ 40% and LVEF ≥ 50% at the time of implantation. We compared the 12-ECG characteristics at the time of device implantation between patients with deterioration of LVEF (≥ 10% reduction) and those without. Twenty-nine patients (25%) had deteriorated LVEF with a decrease in mean LVEF from 59 to 40% during a median follow-up period of 8.9 [4.6–13.7] years. Multivariate logistic regression analysis showed that cumulative % of ventricular pacing [odds ratio (OR) 1.04 per 1% increase, 95% confidence interval (CI) 1.01–1.09, p = 0.04], notching of baseline paced QRS in limb leads (OR 5.04, 95% CI 1.59–19.6, p = 0.005) and the QS pattern in all precordial leads (OR 3.56, 95% CI 1.21–10.8, p = 0.02) were independently associated with deterioration of LVEF. The QS pattern of baseline paced QRS in all precordial leads had 58% sensitivity, 93% specificity for the RV lead position at the tip of RV apex. In conclusion, considering OR by multivariate analysis, notching of baseline paced QRS in limb leads and the QS pattern in all precordial leads at device implantation may be simple and useful predictors to identify patients who are at risk for deterioration of cardiac function during long-term RVAP. 12-ECG monitoring at device implantation and avoidance of the RVAP site showing a QS pattern may be important to prevent deterioration of cardiac function in patients with frequent RVAP.