How Trauma Affects the Brain: The Science Behind PTSD

I remember sitting across from a client, let’s call her Elena, as she told me, “It’s like my body is always waiting for something bad to happen. Even when I know I’m safe, I can’t stop bracing for the worst.”

No loud noises. No danger in sight. Just a sunny afternoon, a warm cup of tea and a nervous system caught in the past.

This is trauma. Not just an event, but a lasting imprint. Not just a memory, but a pattern woven into the fabric of the brain and body. As a therapist, I’ve seen firsthand how trauma can echo long after the moment has passed. And one of the most powerful tools in healing is understanding what’s actually happening in the brain.

So let’s talk about how trauma affects the brain, not just in clinical terms, but in human ones.

Your Brain on Trauma: What’s Going On?

We often think of trauma as something that lives in our past, but the truth is, trauma lives in our present; in our reactions, our bodies, our relationships. It’s a survival response that got stuck in “on” mode.

Three key parts of the brain are at play here: the amygdala, the hippocampus, and the prefrontal cortex.

The Amygdala: The Alarm That Won’t Stop Ringing

Think of the amygdala as your brain’s smoke detector. Its job is to sense danger and get you ready to fight, flee, or freeze. But when you’ve experienced trauma, this system becomes hypersensitive. You don’t just respond to threats, you anticipate them constantly.

Elena told me that just walking through the grocery store made her heart race. There was no obvious threat. But to her amygdala? Something was wrong. Something might happen. So her body prepared for impact, just in case.

The Hippocampus: The Disoriented Storyteller

The hippocampus helps us organize memories and gives them a beginning, middle, and end. After trauma, this system can go offline. Memories become disjointed, foggy, or stuck on repeat. That’s why many people with PTSD don’t just remember their trauma,they relive it.

It’s not that they’re dramatic or dwelling—it’s that their brain hasn’t fully filed the memory away. It's still living in the emergency folder.

The Prefrontal Cortex: The Rational Voice That Goes Silent

Normally, the prefrontal cortex helps us stay calm, make decisions, and tell ourselves, “You’re safe now.” But in moments of PTSD-triggered stress, this part of the brain can shut down. Logic disappears. Emotions take over. It's why someone might know, on paper, that they’re not in danger but still feel terrified.

The Body Remembers, Too

Trauma doesn’t just live in the brain, it lodges in the body. Chronic pain, tension, stomach issues, fatigue, and difficulty sleeping are all common. Many people live in a state of “high alert” without even realizing it. Shoulders are always tight. Breath is shallow. Muscles are clenched. Ready to run or shut down.

The late Dr. Bessel van der Kolk said it best in the title of his book: The Body Keeps the Score. And I see that truth in my therapy room every day.

Trauma and Relationships: When Connection Feels Unsafe

One of trauma’s hardest impacts is how it plays out in our relationships. Because when we don’t feel safe inside ourselves, it’s hard to feel safe with others.

Sometimes trauma survivors become overly vigilant in relationships, watching for signs of betrayal, abandonment, or danger. Others may shut down, fearing intimacy or vulnerability. These patterns are not personality flaws; they are protection strategies. The brain is doing its best to prevent more pain.

Healing Is Not About Forgetting, It’s About Rewiring

Here’s the hope: your brain can change. Truly. Neuroplasticity means that, with the right support, the brain can form new connections. It can learn what safety feels like. It can slowly release its grip on the past.

Therapies like EMDR, somatic experiencing, trauma-informed CBT, and even practices like yoga and mindful breathwork can help re-regulate the nervous system. These approaches work with the body and the brain to restore a sense of grounded presence.

And often, healing begins not with a big breakthrough, but with a moment, like a deep breath that doesn’t feel strained. A morning where the anxiety lifts, even for a little while. A hug that doesn’t make your body tense. These are the quiet victories.

You Are Not Broken, You Are Adapted

If you take anything from this, let it be this: You are not broken. Your brain adapted to survive something painful.

PTSD is not a sign of weakness. It’s a sign of strength, of a brain that worked overtime to protect you. And now, slowly, gently, we can teach it that the danger is over. That safety is possible. That connection is possible.

That you can come home to yourself.

Author: Marisa Gonzalez LMFT-A