Chronic stress, immune imbalance, and thyroid dysfunction are deeply interconnected. This forms a stress–immune–thyroid triad where each system influences the others, affecting energy, mood, and resilience. Research shows that targeted support—including adaptogens, micronutrients can help restore communication across this network. Rather than offering quick fixes, this systems-based approach addresses underlying feedback loops, combining clinical insight, patient engagement, and supportive lifestyle practices to rebuild physiological balance and improve well-being over time.
Allison Sayre, WHNP
From menarche to menopause, regular menstrual cycles are often referenced to as a sign of health and homeostasis in the female body. When periods change or disappear without pregnancy or menopause, it can be a sign that the body is under physical or psychological stress. One of the most common but under-recognized causes of missing periods for otherwise healthy women is Functional Hypothalamic Amenorrhea (FHA).
FHA occurs when the hypothalamus puts the possibility of reproduction on pause. It’s the body’s way of saying: conditions are not safe to sustain a pregnancy right now. The triggers are usually related to physical stressors such as energy deficit (undereating or over-exercising), psychological stress, or a combination of the two. [1]
While amenorrhea and infertility are the main clinical features of this diagnosis, the effects of FHA are wider reaching. Hypoestrogenemia (low estrogen), subclinical hypothyroidism, and other factors caused by the disorder impact bone, cardiovascular, psychological, cognitive, and metabolic health. [2] Here, specifically, we will explore the connection between FHA and thyroid function. Understanding this link can help women address the root causes of amenorrhea and support whole-body healing.
What Is Functional Hypothalamic Amenorrhea?
FHA is defined as the absence of menstrual cycles for at least three months due to suppression of the hypothalamic-pituitary-ovarian (HPO) axis. [1] In other words, the brain stops sending the hormonal signals that trigger ovulation and menstruation.
Unlike other causes of amenorrhea (like polycystic ovary syndrome/PCOS or premature ovarian failure), FHA is not due to structural or functional issues with the ovaries or uterus. It’s the body’s adaptive response to perceived scarcity or acute stress, when the demands of a pregnancy could potentially threaten a woman’s survival. [1]
Common triggers include:
- Low energy availability (not enough calories to meet energy demands
- Excessive exercise without adequate recovery
- Psychological stress or trauma
- Specific nutrient deficiencies [2]
The Body’s Priorities
From an evolutionary standpoint, when resources are limited, reproduction is optional, but survival is non-negotiable. Because of this, the hypothalamus has become highly attuned to changes in energy availability. When fuel is scarce, energy-intensive processes like reproduction could be dangerous. So instead, energy is diverted to the most vital systems (fueling the brain and maintaining blood pressure for vital organ function) and metabolism is regulated to parse energy as efficiently as possible. This is where the mechanism connecting FHA and thyroid health becomes clear.
The Hypothalamus, Reproduction, Metabolism, and Beyond
The hypothalamus orchestrates both reproductive and thyroid function, through the hypothalamic-pituitary-ovarian axis and the hypothalamic-pituitary-thyroid axis, respectively. It releases gonadotropin-releasing hormone (GnRH) to stimulate ovulation and thyrotropin-releasing hormone (TRH) to stimulate thyroid activity. Stress suppresses hypothalamic activity, and therefore function of these axes, and secretion of these stimulatory hormones are also suppressed. Loss or reduction in these hormones can result in sporadic or absent ovulation (amenorrhea) and slowed thyroid function (presenting as subclinical hypothyroidism). [3]
Essentially, FHA and thyroid dysfunction can both stem from the hypothalamus detecting that the body doesn’t have enough resources to sustain both a pregnancy and a woman’s metabolism at the same time.
And the consequences of FHA do not stop at infertility. A downstream effect of low GnRH is low estrogen (hypoestrogenemia), which plays a role in both cardiovascular and bone health. This is because estrogen normally helps keep blood vessels flexible and supports healthy cholesterol balance, so when levels drop, the risk of stiff arteries and unfavorable lipid changes can occur. In bone tissue, estrogen slows bone breakdown and promotes bone density maintenance. Without it, bone resorption accelerates, leading to weaker bones and higher fracture risk.
Additionally, thyroid hormones also contribute to healthy bone turnover, with low thyroid levels further exacerbating issues with bone density. For these reasons, it is no surprise that women with FHA have a significantly higher risk for cardiovascular issues and low bone density than peers without an FHA diagnosis. [1]
Thyroid Adaptations in FHA
Research shows that women with FHA often exhibit:
- Lower free T3 (triiodothyronine) levels, but normal rT3: T3 is the active thyroid hormone responsible for energy metabolism. The body reduces T3 as a way to slow metabolism and conserve fuel. [3]
- Lower T4 (thyroxine): Total T4 and free T4 both trend downward. [3]
- Normal TSH (thyroid stimulating hormone): Unlike true hypothyroidism, TSH may remain in the normal range. [3]
These characteristics, along with a decrease in leptin, help identify the issue as “adaptive hypothyroidism” as they reflect an energy-conserving shift, not a true problem with thyroid function. [3] Thyroid hormone imbalance, in this case, is an adjustment to stress driven by the brain.
Why the Thyroid Link Matters
The thyroid-reproductive connection matters for two key reasons:
- Diagnosis: Women with FHA may be misdiagnosed with thyroid disease when the real issue is energy imbalance and hypothalamic suppression. While hypothyroidism can cause amenorrhea, in the context of FHA, it is not the cause, but a symptom. Treating only the thyroid misses the bigger picture. [2]
- Whole-body symptoms: FHA is not just the absence of periods. Low thyroid signaling contributes to fatigue, cold intolerance, constipation, hair loss, and a low mood, which are also all symptoms that often accompany amenorrhea. Recognizing the thyroid piece helps validate why women may feel “off” in more ways than one.
Restoring Balance
The good news is that FHA is usually reversible once the stressors are addressed. The Endocrine Society’s guidelines suggest menses should return within 6-12 months of adequate lifestyle modification. [2] Whenever feasible, the treatment approach should be multidisciplinary, and include a practitioner, a dietician, and mental health provider. Here are key strategies:
1. Increase Energy Availability and Nutrient Density
Consider the specific foods and portions being included in the diet. A woman needs calories to support both activity and basic metabolic needs, the abundance of which is unique to each individual. The general “2000 calories a day” rule-of-thumb may be too much for someone of petite stature or a sedentary lifestyle, and not nearly enough for an athlete or someone built with a larger frame. A conversation between practitioner and patient should take place to determine a daily caloric goal.
While caloric input is important, so is the balance of nutrients, both macro and micro, found in the diet. A person needs adequate protein, fats, and complex carbohydrates, as well as a balance of essential vitamins and minerals for optimal function. Choose foods wisely based on not only calorie count, but also nutrient density. Consider evaluating current nutritional status by blood test and navigate dietary changes accordingly.
2. Rethink Exercise
Bodies need regular movement for optimal health, so rather than stopping, consider slowing down. This could be slowing the pace, distance, or frequency of cardiovascular activities, or the replacement of high-intensity training with gentler movements, like yoga, walking, or restorative exercise. Incorporate rest days in an exercise plan to allow the body to repair.
3. Manage Stress
This is where a mental health provider can make a big difference. Ideally, managing stress would entail naming and eliminating stressors. In many cases, stressors (work or familial responsibilities, etc.) cannot be eliminated, so the way a person reacts and processes them must change. Mind-body practices such as meditation and breathwork, CBT therapy, and journaling have clinical data to back their use for the reduction of hypothalamic stress signals. [4]
4. Prioritize Sleep
In addition, adequate sleep is non-negotiable for hypothalamic hormone balance. [5] Like caloric needs, the amount of quality sleep needed by each individual is also fairly unique. However, not getting the amount required has physiological consequences for the endocrine system.
Professional Intervention
If a menstruating person has missed three or more periods, medical evaluation is important. A healthcare provider can rule out other causes of amenorrhea, check thyroid labs, and assess for nutritional deficiencies.
Functional testing can also provide a more nuanced picture of thyroid activity, including free T3, reverse T3, T4, free T4, TSH, thyroid antibodies, and adrenal hormones. These numbers can determine whether thyroid adaptations are part of FHA or if there’s an independent thyroid condition that needs to be addressed directly. [3]
Final Thoughts
For women, the menstrual cycle is a window into overall health. Missing periods are not just a reproductive issue; they are a red flag for broader health issues and imbalances in the body.
Recognizing the connection between Functional Hypothalamic Amenorrhea and thyroid function helps us understand the body’s incredible ability to adapt. Importantly, it is also an example of how physical symptoms, disconnected from the whole person, can be deceiving. As practitioners, it is so important to consider the deepest possible root cause and the connection of body and mind. Only then can balance be restored without unnecessary intervention.
Disclaimer:
The information provided is for educational purposes only. Consult your physician or healthcare practitioner if you have specific questions before instituting any changes in your daily lifestyle including changes in diet, exercise, and supplement use.
Allison Sayre is a board-certified women’s health nurse practitioner with advanced expertise in hormonal health, integrative gynecology, and patient-centered care across the lifespan. She holds a Master of Science in Nursing and has served as both a clinical provider and educator in functional and conventional women’s health settings.
Allison has led clinical programming, practitioner training, and content development for leading health brands and organizations. Her work bridges the clinical and commercial worlds, helping translate scientific evidence into practical tools for healthcare practitioners. At ARG, Allison contributes to medical education, clinical protocol development, and strategic content that supports the evolving needs of women's healthcare practitioners.