A part of the brain linked to emotions and empathy, called the insula, was found to be particularly small in girls who had suffered trauma.
But in traumatised boys, the insula was larger than usual.
This could explain why girls are more likely than boys to develop post-traumatic stress disorder (PTSD), the researchers said.
Their findings suggest that boys and girls could display contrasting symptoms after a particularly distressing or frightening event, and should be treated differently as a result.
The research team, from Stanford University School of Medicine, said girls who develop PTSD may actually be suffering from a faster than normal ageing of one part of the insula - an area of the brain which processes feelings and pain.
The insula, or insular cortex, is a diverse and complex area, located deep within the brain which has many connections.
As well as processing emotions, it plays an important role in detecting cues from other parts of the body.
The researchers scanned the brains of 59 children aged nine to 17 for their study, published in Depression and Anxiety.
One group, of 14 girls and 16 boys, had suffered at least one episode of severe stress or trauma while a second group, of 15 girls and 14 boys, had not been exposed to any.
In the group of traumatised boys and girls, there was evidence that one area of the insula - the anterior circular sulcus - had changed in size and volume compared with the group with no trauma.
This shows that the insula is changed by exposure to acute or long-term stress and plays a key role in the development of PTSD, the researchers said.
Lead study author Dr Megan Klabunde said it was important to consider the different physical and emotional reactions to stressful events.
"It is important that people who work with traumatised youth consider the sex differences.
"Our findings suggest it is possible that boys and girls could exhibit different trauma symptoms and that they might benefit from different approaches to treatment."
And she added: "There are some studies suggesting that high levels of stress could contribute to early puberty in girls."
Dr Klabunde said they would now look at other regions of the brain connected to the insula to see if they could detect similar changes.
What is PTSD?
Post-traumatic stress disorder is the term used to described the psychological effects of being involved in a traumatic event, such as a major car accident, a natural disaster, bullying, abuse or violent crime.
Many young people who experience very distressing events recover without experiencing PTSD - but some people do develop it.
Symptoms can include:
- Flashbacks and nightmares
- Avoiding reliving the event
- Anxiety, unable to relax
- Problems sleeping
- Problems eating
The charity Young Minds says it is normal to experience symptoms for a few weeks after a distressing event but if you are still having symptoms after a month, it is a good idea to talk to your GP who should offer you some therapy to deal with your thoughts and behaviour.