Sinus node dysfunction (SND) with junctional rhythm (JR) is common after the Fontan operation. Atrial pacing (AP) restores atrioventricular (AV) synchrony, but the placement of a pacemaker carries significant morbidity. To study the impact of AP on echocardiographic parameters of function in Fontan patients with SND and JR. Nine Fontan patients with AP for SND and JR were prospectively studied with echocardiography in the following conditions—baseline paced rhythm, underlying JR and, if possible, slow-paced rhythm below their baseline paced rate (~ 10 bpm faster than their JR rate). Cardiac index was significantly lower in JR (3 ± 1.1 L/min/m²) vs AP (4.2 ± 1.4 L/min/m²; p = 0.002). Diastolic function also significantly worsened with increased ratio of early diastolic systemic AV valve inflow velocity to early diastolic systemic AV valve annulus velocity (E/e′ ratio) by tissue Doppler imaging (TDI) in JR (11.6 ± 4.6) vs AP (8.8 ± 2.2, p = 0.016). Pulmonary venous flow reversal was present in 7/9 patients in JR vs 0/9 in AP (p = 0.016). There were no significant differences in these echocardiographic measurements between the paced and slow-paced conditions. When compared to AP, JR was associated with a significant reduction in cardiac output and diastolic function, and an increased prevalence of pulmonary vein flow reversal. There were no differences between paced and slow-paced conditions, suggesting that AV synchrony rather than heart rate was primarily contributing to cardiac output. Further studies are needed to understand the chronic impact of JR on Fontan outcomes.