Objective To investigate somatic growth of children undergoing stageⅡ Fontan procedure. Methods Clinical data of 152 children who underwent stageⅡ Fontan procedure in Shanghai Children’s Medical Center, Shanghai Jiaotong University School of Medicine between January 2012 and December 2015 were reviewed. There were 84 males and 68 females at age of 4-16 years. The weight and height of those children in each operative stage were assessed, and WHO Z-score was obtained to describe the pattern of growth of the children. Results Mean weight for age Z-score (WAZ) and height for age Z-score (HAZ) were –0.73 and 0.06 at birth, –1.27±1.37 and –1.27±1.72 before Glenn procedure, –0.47±1.08 and –0.69±1.17 before Fontan procedure, –0.42±1.18 and –0.39±1.48 at follow-up, respectively. A significant decline (P<0.05) in WAZ and HAZ was found before Glenn procedure. After the Glenn procedure, there was significant catch-up growth (P<0.05). The WAZ was stabilized after Fontan procedure, while the HAZ was reversed (P<0.05) continually. Conclusion The somatic growth is impaired in children with stageⅡ Fontan procedure. There is a trough of growth before Glenn procedure. Although catch-up growth occurs after Glenn procedure, low body weight and growth retardation remain at follow-up. Effective interventions such as more intensive nutritional strategies before Glenn procedure should be targeted at those children in the future, so as to improve their growth.