Introduction. Right ventricular apical pacing (RVAP) has a greater ‘desynchronizing effect’ than pacing from the interventricular septum (RVSP) and may translate into worse outcomes in the long run. The aim of the present study was to examine the short- and intermediate-term effects of RVAP versus RVSP on echocardiographic features, left ventricular function, and clinical outcome. Materials and methods. 467 patients between August 2014 and March 2018 without structural heart disease were prospectively randomised to RVAP (N = 226) or RVSP (N = 241) and were studied at baseline, six months, and 12 months by echocardiography, biochemically [N-terminal pro-B-type natriuretic peptide (NT-proBNP)], and clinically [six-minute walk test (6MWT)]. Left ventricular 2D strain and tissue velocity images were analysed to measure 18-segment time-to-peak longitudinal systolic strain and 12-segment time-to-peak systolic tissue velocity. Intraventricular dyssynchrony was calculated using tissue Doppler velocity data by comparing the time to systolic peak velocity between segments in multiple apical views by their respective standard deviations. Interventricular dyssynchrony was measured as the temporal difference of left ventricular pre-ejection period and right ventricular pre-ejection period by pulse-wave Doppler images. All the analysis was carried out using statistical package for social service version 17.0 (SPSS Inc., Chicago, IL, USA). A p-value < 0.05 was considered statistically significant. Results. The commonest indication for pacemaker implantation was atrioventricular block (N = 311, 66.6%), followed by sinus node dysfunction (N = 138, 29.5%) and chronic bifascicular and trifascicular block (N = 18, 3.9%), with all patients receiving a single chamber pacemaker (VVI: n = 107, 22.9% and VVIR: n = 360,77.1%). There were significant differences in NT-proBNP level (410 ± 254 pg/mL vs. 370 ± 168 pg/mL, p = 0.02), 6MWT (442 ± 19 m vs. 482 ± 21 m, p = 0.01), mean QRS duration (164 ± 8.3 ms vs. 148 ± 10.6 ms, p = 0.02), intraventricular dyssynchrony (septal to lateral wall delay: 88.6 ± 24.2 ms vs. 43.7 ± 11.2 ms, p = 0.04), interventricular dyssynchrony (31.2 ± 22.8 vs. 19.4 ± 11.2, 0 = 0.03), end diastolic volume (78.4 ± 15.6 mL vs. 72.8 ± 14.2 mL, p = 0.04), and end-systolic volume (30.2 ± 13.1 mL vs. 25.6 ± 11.7 mL, p = 0.05) at the end of 12 months between RVAP and RVSP respectively, though not significantly different at six months, favouring the RVS-paced group. However, no significant difference in ejection fraction (59 ± 5% vs. 61.5 ± 3.2%, p = 0.39) and New York Heart Association class (1.29 ± 0.3 vs. 1.28 ± 0.4, p = 0.3) at six and 12 months follow up were noted. Conclusion. Right ventricular septal pacing was associated with a better outcome in terms of echocardiographic indices, left ventricular function, and clinical outcome compared to patients with apical pacing over an intermediate-term follow up.