Background: Pregnancy in women with Fontan physiology poses a significant management challenge and is deemed high risk. The aim of this study is to describe short and long-term pregnancy outcomes in women who have undergone Fontan palliation and propose a novel risk-stratification model specific to women with a Fontan heart. Methods: We undertook a single-centre, retrospective cohort study of all female Fontan patients (n = 78) from 1991-2015. We recorded pregnancy outcome, maternal cardiovascular and obstetric complications and fetal outcome. We propose a risk stratification model to identify those women who might be at highest risk of adverse outcomes during pregnancy. Results: Twenty-one women had 55 pregnancies, with 13 (24%) live births and 38 (69%) spontaneous miscarriages (p < 0.001). Eight (62%) out of 13 live birth pregnancies incurred maternal cardiovascular complications and six (46%) experienced maternal obstetric complications. Median gestational age at delivery was 32(27-39) weeks with 12 out of 13 (92%) pregnancies resulting in pre-term delivery. There were more pregnancies (OR 4.90, 95% CI 1.46-16.42, p ≤ 0.01) and a trend towards a higher proportion of live births (OR 7.60, 95% CI 1.81-31.97, p = 0.06), in the 'lower risk' compared to those women in the 'very high risk' group. There were no maternal deaths. Conclusions: We observed a high first trimester miscarriage rate, significant maternal cardiovascular and obstetric complication rates and a high rate of pre-term births in pregnant Fontan women. Our risk stratification model requires further investigation but may identify those women at particularly high risk of a poor outcome, and inform realistic pre-pregnancy counselling.