An analysis of data on 38,000 individuals found those born by Caesarean section were 22% more likely to be obese than those who had natural births.
They had a 26% greater chance of being overweight, as defined by their body mass index.
Scientists warned mothers to be aware of the possible long-term consequences of Caesareans.
Effects of a surgery-assisted birth on a baby's gut bacteria and genes could be two reasons for the trend, they believe. Professor Neena Modi, from Imperial College London, said: "There are good reasons why C-section may be the best option for many mothers and their babies, and C-sections can on occasion be life-saving.
"However, we need to understand the long-term outcomes in order to provide the best advice to women who are considering Caesarean delivery.
"This study shows that babies born by C-section are more likely to be overweight or obese later in life. We now need to determine whether this is the result of the C-section, or if other reasons explain the association."