The Neurobiology of Trauma

What your brain does under threat—and what healing looks like.

• Trauma hijacks the brain’s survival systems, shutting down higher-order thinking.

• Freezing and dissociation are survival strategies, not failures.

• PTSD disrupts the brain’s ability to “turn off” the alarm.

• Evidence-based PTSD treatments restore the brains ability to modulate the threat response.

Have you ever questioned why you—or someone close to you—froze, went numb, or seemed to shut down in the midst of trauma? Maybe you’ve replayed the moment, asking, “Why didn’t I fight back? Why didn’t I run?” Or perhaps you’ve noticed that, even long after the event, your brain and body react to reminders as if the danger is happening all over again.

If any of this sounds familiar, you’re not alone. These are questions that linger for many survivors, and the answers are rooted in the very structure of our brains.

When Survival Takes Over

When your brain detects danger, it flips a switch: survival mode. Suddenly, digestion, complex thinking, and even speech is dialed down. The prefrontal cortex (PFC)—the part of your brain responsible for planning, reasoning, and self-control—goes offline. All available energy is rerouted to immediate reaction.

The phrase “fight or flight” gets thrown around a lot, but it’s often misunderstood. Originally, it described a physiological state: Your sympathetic nervous system floods your body with adrenaline, prepping you to react (Hopper, 2021).

In fact, most people don’t fight or run during an assault. Instead, the brain defaults to whatever reflexes or habits it’s learned—sometimes fighting or fleeing, but often freezing, submitting, or dissociating. It is unusual to fight or flee while being assaulted!

Why Freezing Happens

Within seconds of a threat, your prefrontal cortex is impaired. The brain’s defense circuitry takes over, running on reflexes and habits.

If you’ve learned to appease, submit, or go silent in the face of aggression, those habits may kick in automatically. Sometimes, the body freezes—muscles go rigid (tonic immobility), or limp (collapsed immobility). You might feel numb, disconnected, or “out of your body.”

This isn’t weakness; it’s evolution’s way of keeping you alive. Check out this old account of David Livingstone being attacked by a lion in the 1800s:

Growling horribly close to my ear, he shook me as a terrier dog does a rat. The shock produced a stupor similar to that which seems to be felt by a mouse after the first shake of the cat. It caused a sort of dreaminess, in which there was no sense of pain nor feeling of terror, though quite conscious of all that was happening. It was like what patients partially under the influence of chloroform describe, who see all the operation, but feel not the knife. This singular condition was not the result of any mental process. The shake annihilated fear, and allowed no sense of horror in looking round at the beast. This peculiar state is probably produced in all animals killed by the carnivora; and if so, is a merciful provision by our benevolent Creator for lessening the pain of death. (Livingstone, 1857)

What self-protection habits did you learn growing up? How do you notice your body reacting similarly to stress or threat?

Disrupted Feedback Loop: When Brains Get Stuck

In a well-modulated threat response, the amygdala (the brain’s alarm center) detects threat, and the body reacts--we don't get to weigh in with logic or careful planning. Once the threat passes, the prefrontal cortex (the brain's executive functioning center) tells the amygdala to stand down.

With PTSD, the amygdala shows heightened responsivity while the PFC shows decreased activity. Because the PFC is not functioning properly, there is no message sent back to the amygdala to stop the threat response. The amygdala stays on high alert, and the prefrontal cortex struggles to regain control. This means strong emotional reactions, trouble making decisions, and difficulty recognizing when you’re actually safe (Resick, Monson, & Chard, 2017).

The prefrontal cortex isn’t fully developed until your mid-20s. This means children and teens have fewer resources to process trauma and may develop trauma-related beliefs or habits that stick with them into adulthood. Many adult survivors are still operating from the “rules” their brains created when they were young and vulnerable (Resick, Monson, & Chard, 2017).

Healing: Rewiring the Brain Through Evidence-Based PTSD Treatment

Recovery is possible. Evidence-based therapies like cognitive processing therapy (CPT) and prolonged exposure (PE) have been examined through fMRI studies, and have been shown to be actively retraining our brains (Abdallah et al, 2019; Fonzo et al, 2021).

In these treatments, you talk about the trauma in a way that keeps your prefrontal cortex engaged—naming emotions, examining thoughts, and gradually making sense of what happened. By talking through traumatic events in a structured, supportive way, we keep the prefrontal cortex (PFC) “online.” This means the part of the brain responsible for reasoning, reflection, and self-control stays engaged, even as the trauma circuit is activated.

This process helps rebuild the connection between your PFC and your amygdala, restoring the brain's ability to calm the survival response. As we revisit difficult memories, the PFC and amygdala are both active, but instead of the amygdala running wild with overwhelming emotion, the PFC helps modulate and contextualize those feelings.

Over time, this repeated practice strengthens the connection between the PFC and amygdala. The result? The amygdala becomes less likely to trigger extreme emotional responses, and the brain learns that it’s possible to feel, reflect, and stay grounded—all at once.

This is why these therapies are so effective: they help the brain practice regulation, not just recall. As you put words to your experience, you’re not just telling your story—you’re literally rewiring your brain: "Name it to tame it" (Resick, Monson, & Chard, 2017).

In the process of healing, we learn that our trauma reactions were our brains doing their best to keep us alive. Now, with support and practice, we can teach our brains a new way to be.

Jaimie Lusk, Psy.D., - Website - Blog -

References

Abdallah, C. G., Averill, C. L., Ramage, A. E., Averill, L. A., Alkin, E., Nemati, S., ... & STRONG STAR Consortium. (2019). Reduced salience and enhanced central executive connectivity following PTSD treatment. Chronic Stress, 3, 2470547019838971.

Hopper, J. (n.d.). Jim Hopper, Ph.D.

Hopper, J. [Jim Hopper, PhD]. (n.d.). Jim Hopper, PhD [YouTube channel]. YouTube.

Hopper, J. (2021, February 8). Reflexes and habits is much better than “fight or flight.” Psychology Today.

Livingstone, D. (1857). Missionary travels and researches in South Africa.

Fonzo, G. A., Goodkind, M. S., Oathes, D. J., Zaiko, Y. V., Harvey, M., Peng, K. K., ... & Etkin, A. (2021). Amygdala and insula connectivity changes following psychotherapy for posttraumatic stress disorder: a randomized clinical trial. Biological Psychiatry, 89(9), 857-867.

Resick, P. A., Monson, C. M., & Chard, K. M. (2017). Cognitive Processing Therapy for PTSD: A Comprehensive Therapist Manual (2nd ed.).