Objectives: Conduction system pacing (CSP) and atrioventricular junction ablation (AVJA) improve the outcomes in patients with symptomatic, refractory atrial fibrillation (AF). In this setting, AVJA can be performed simultaneously with implantation or in a second procedure a few weeks after implantation. Comparison data on these two alternative strategies are lacking. Methods: A prospective, multicentre, observational study enrolled consecutive patients with symptomatic, refractory AF undergoing CSP and AVJA performed in a single procedure or in two separate procedures. Data on the long-term outcomes and healthcare resource utilization were prospectively collected. Results: A total of 147 patients were enrolled: for 105 patients, CSP implantation and AVJA were performed simultaneously (concomitant AVJA); in 42, AVJA was performed in a second procedure, with a mean of 28.8 ± 19.3 days from implantation (delayed AVJA). After a mean follow-up of 12 months, the rate of procedure-related complications was similar in both groups (3.8% vs. 2.4%; p = 0.666). Concomitant AVJA was associated with a lower number of procedure-related hospitalizations per patient (1.0 ± 0.1 vs. 2.0 ± 0.3; p < 0.001) and with a lower number of hospital treatment days per patient (4.7 ± 1.8 vs. 7.4 ± 1.9; p < 0.001). Conclusions: Concomitant AVJA resulted as being as safe as delayed AVJA and was associated with a lower utilization of healthcare resources.