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When the Body Hits Pause: Understanding Functional Hypothalamic Amenorrhea

When the Body Hits Pause: Understanding Functional Hypothalamic Amenorrhea

Tracy Tranchitella is a Doctor of Naturopathic Medicine integrating the scientific principles of Functional Medicine with the sensibility and holistic view of traditional naturopathy. Tracy Tranchitella, ND – Sunrise Functional Medicine

A regular menstrual cycle is often described as a “vital sign” of health—and for good reason. It reflects a delicate and ongoing conversation between the brain, hormones, metabolism, stress levels, and overall energy availability. When that conversation is disrupted, one of the first signals can be a missing period.

Dr. Tracy Tranchitella, ND works with women who are surprised—and often unsettled—when their menstrual cycle quietly disappears. For many, this isn’t due to pregnancy or menopause, but to a lesser-known condition called Functional Hypothalamic Amenorrhea (FHA). While the name sounds technical, the story behind FHA is deeply human—and increasingly common.

What does it mean when a period stops?

Amenorrhea is the medical term for the absence of menstruation in a woman of reproductive age. It can be primary, meaning menstruation never begins by the expected age, or secondary, when periods stop for three months or longer in someone who previously cycled regularly. There are times when amenorrhea is normal—during pregnancy, breastfeeding, or after menopause. But outside of those windows, a missing period is the body’s way of waving a small but meaningful red flag.

In functional hypothalamic amenorrhea, that signal isn’t caused by structural problems or permanent damage. Instead, it reflects a functional shutdown of the brain’s reproductive signaling—specifically within the hypothalamic-pituitary-ovarian (HPO) axis.

Why the brain puts reproduction on hold

Reproduction is energy-intensive. When the body perceives that resources are scarce or stress is overwhelming, it makes a protective decision: survival first, reproduction later. FHA most often develops in the context of:

  • Chronic psychological stress
  • Excessive or intense exercise
  • Inadequate caloric intake or disordered eating
  • Or, more commonly, a combination of all three

This pattern shows up frequently in high-achieving women, athletes, perfectionists, and those who are deeply committed to “doing everything right” for their health—sometimes to the point of imbalance. Under these conditions, the hypothalamus reduces its release of gonadotropin-releasing hormone (GnRH). That single shift has a cascade effect: lower follicle-stimulating hormone (FSH), lower luteinizing hormone (LH), suppressed ovulation, and low estrogen levels. The result? A cycle that simply stops.

Stress hormones, energy balance, and a missing period

One of the key messengers involved in FHA is kisspeptin, a neuropeptide that helps signal the brain to initiate reproductive hormone release. Kisspeptin is exquisitely sensitive to both stress and energy availability. When stress hormones like cortisol rise—whether from emotional stress, under-fueling, or overtraining—kisspeptin signaling drops. At the same time, hormones involved in appetite and metabolism shift. Leptin, which signals satiety and adequate energy stores, decreases with low body weight or calorie intake. Ghrelin, the hunger hormone, rises. Together, these signals tell the brain that now is not the time to support reproduction.

In some women, genetic factors may increase susceptibility to this shutdown, which helps explain why not everyone who exercises intensely or eats restrictively develops FHA.

FHA is not “just” a menstrual issue

While the loss of a period is often what brings women into care, FHA affects far more than the reproductive system. Low estrogen levels influence:

  • Fertility, through anovulation and increased miscarriage risk
  • Bone health, increasing the likelihood of low bone density and stress fractures
  • Cardiovascular health, through changes in blood vessel function and lipid profiles
  • Brain health and mood, contributing to anxiety, low mood, and cognitive changes

Many women with FHA describe feeling emotionally flat, more anxious, or mentally foggy—experiences that mirror what some women notice during menopause. This isn’t a coincidence. Estrogen plays a powerful role in neurotransmitter balance and brain function at every life stage.

How FHA is evaluated in functional medicine

Diagnosing FHA is largely a process of exclusion, but a thoughtful workup provides clarity and reassurance. In addition to ruling out pregnancy, evaluation often includes hormone testing to assess estrogen, FSH, LH, thyroid function, prolactin, and androgens, along with a detailed review of lifestyle, nutrition, exercise habits, and stress load. From a functional medicine perspective, additional testing may help illuminate contributing factors. This can include assessments of cortisol rhythm, micronutrient status, thyroid hormones, and metabolic markers—each offering insight into how the body is responding to stress and energy demands.

Just as important is understanding the story behind the labs. Numbers alone don’t explain why the system shut down; context does.

Supporting recovery begins with safety

The cornerstone of FHA treatment is restoring the body’s sense of safety and sufficiency. That often means:

  • Increasing caloric intake with nutrient-dense foods
  • Moderating or temporarily reducing intense exercise
  • Actively addressing psychological stress
  • Supporting healthy sleep and nervous system regulation

In some cases, even modest weight restoration can be enough to restart hormonal signaling. For others, the process takes time—and patience. When lifestyle shifts alone are not sufficient, carefully guided hormone support may be considered to protect bone health and support cognitive and emotional well-being while deeper healing occurs. Importantly, this approach is different from using oral contraceptives, which can mask symptoms without restoring natural ovulatory function.

Nutritional support and botanicals may also play a role, but they are most effective when foundational needs—energy, safety, and stress regulation—are already being addressed.

Listening when the body whispers

Functional hypothalamic amenorrhea is not a failure of the body—it is an adaptive response. The body is doing exactly what it was designed to do when it senses threat or scarcity.

As Dr. Tracy Tranchitella emphasizes in her work at Sunrise Functional Medicine, a missing period is not something to ignore or override. It’s information. And when approached with curiosity rather than judgment, it can become an opportunity to restore balance, resilience, and long-term health. In a world that often rewards pushing harder, FHA is a reminder that the body values sustainability over perfection—and that true wellness includes knowing when to pause. Learn more and request a consultation >>