Abstract Background Exercise intolerance is frequent among Fontan patients and an important determinant for quality of life. This study investigated the hemodynamic causes of impaired exercise capacity in Fontan patients with particular focus on the influence of stroke volume index (SVI) and heart rate (HR). Methods and results In 38 Fontan patients, peak oxygen consumption (VO2 ), SVI and HR were recorded during incremental load exercise test and compared with 19 age and gender matched controls. SVI (ml/m2 ) was lower in patients than controls during warm-up (2826–31 vs. 3530–39, p = 0.0093), at submaximal (4037–43 vs. 5551–59, p < 0.0001) and at maximal exercise (3835–40 vs. 5451–58, p < 0.0001). Similarly, HR (% of expected maximum) was lower in patients at warm-up (4543–48% vs. 6457–64%, p < 0.0001), submaximal (7168–75% vs 8582–88%, p < 0.0001) and maximal exercise (8480–88% vs. 9795–99%, p < 0.0001). Furthermore, SVI dropped 14% (from 4441–48 to 3835–40 ml/m2 ) in Fontan patients from the peak plateau to maximal exercise vs. 5% (from 5753–61 to 5451–58 ml/m2 ) in controls, p < 0.0001. The low SVI and HR explained 67% and 20% of the difference in peak VO2 between Fontan patients and controls respectively. Conclusion SVI decreased significantly in Fontan patients near the end of maximal effort exercise. The low SVI at maximal exercise was the most important hemodynamic factor limiting exercise capacity in Fontan patients, whereas chronotropic impairment had a smaller impact. The low SVI and HR at maximal exercise accounted for the difference in peak VO2 between Fontan patients and controls in this study. Clinical trial registration http://www.cvk.sum.dk/CVK/Home/English.aspx (protocol nr: H-3-2010-045).