Objectives The Fontan procedure remains the predominant palliative approach for a single ventricle circulation despite many concerns about long-term elevation of systemic venous pressures on multiple organ systems. Preservation of cardiac function is a prerequisite for health of the Fontan circuit and loss of sinus rhythm with need for implantation of a permanent pacemaker remains a concern. We sought to compare early and late survival, complications and need for further intervention between those patients who require a permanent pacemaker and patients who remain in sinus rhythm following the Fontan procedure. Methods This single centre, retrospective case note analysis study involved all patients who have undergone the Fontan procedure between 1987 and 2015 and have had regular follow up at Leeds General Infirmary. 145 patients were identified of which two were excluded for having a pacemaker prior to surgery. Of the remainder, 21 patients required a pacemaker. The primary outcome was survival and the secondary outcomes were early and late complications, need for further intervention and oxygen saturation in long-term follow up. Results There was no difference in survival at 7 days, 30 days, 1 year or 5 years (30 day survival SR 92.6%, non-SR 90.5%, p=0.66). The pacemaker group were more likely to have cerebral or renal complications in the first year post procedure but there was no difference in long term complications such as protein losing enteropathy or pulmonary hypertension (acute kidney injury SR 0.8%, non-SR 19.1%, p=0.002). Patients in the pacemaker group were more likely to undergo further interventions and these interventions were more likely to involve cardiopulmonary bypass (SR 0.06%, non-SR 0.48%, p Conclusions This study demonstrates the likely cause of loss of sinus rhythm being more complex surgery performed as part of the Fontan procedure. With more active surgical management of these issues in early childhood as well as preference for an extracardiac conduit loss of sinus rhythm is likely to become a less frequent issue. Despite an increase in early complications and the need for further interventions, pacemaker requirement does not affect long term outcome of the Fontan procedure.