“Aromatherapy works fairly well for autoimmune diseases. (These conditions are often the result of many years of assault on the body that led to seriously impaired or permanently destroyed body functions.)” - Kurt Schnaubelt PhD (founder and scientific director of the Pacific Institute of Aromatherapy in San Francisco), Medical Aromatherapy: Healing with Essential Oils, page 252.

“Conditions attributed to Epstein-Barr virus, like chronic fatigue syndrome and fibromyalgia have been treated with aromatherapy. Strong immunostimulant essential oils such as Oregano, Thyme, Clove, or best of all, Cinnamon should be used in a tolerable fashion, which means taking frequent small dosages. Cinnamon oil can be dissolved in an edible vegetable oil and ingested in capsule form. The dosage per capsule or per application should not be above 1 to 2 drops. The maximum recommended dosage for these capsules for day one and two of the treatment is 10 x 1 drops (10 drops per day). Using these capsules maybe five or six times a day is sufficient. On the third day, the dosage should be cut in half so that a maximum of 5 x 1 drop per day of oil is taken and the other part being substituted with a single essential oil within the group of the terpene alcohol essential oils: Palmarosa, Tea Tree, or Ravensara aromatic are good choices. The variation between essential oils and different mixes of essential oils, all of which should be high in terpene alcohols, will be more effective than the use of a single essential oil to which the body might adjust in a certain way. This rather broadly designed treatment has been implemented in many alternative practice situations and, given the diffuse nature of these conditions, the results were encouraging."

"If balancing of the intestinal flora is the goal of the treatment, these stronger essential oils might need to be taken over two to three weeks. These oils are tolerated quite well internally and different practices report different dosages ranging from 1-10 drops of essential oil per day.”

“Moroccan Thyme (Thymus satureioides) May be the most effective for chronic infections and/ or autoimmune diseases. It helps realign the immune system reducing chronic inflammation caused by pathologically elevated levels of gamma globulins. Aromamedicine uses this oil for angina and tuberculosis. Because of its highly restorative combination of carvacrol (a phenol) and borneol (a valuable terpene alcohol not encountered in similarly high concentrations in any other oil), it has also been recommended for arthrosis. Moreover, it is a sexual stimulant.”
Schnaubelt, Kurt, Medical Aromatherapy: Healing with Essential Oils, page 203.

"If inflammative processes are prevalent, essences with high proportions of aldehydes are recommended. Excess mucous can be addressed with ketone containing essential oils. Essential oils allow highly adequate management of virus conditions. Pierre Franchomme suggests to treat Epstein-Barr Virus (EBV) with the same strategy as a flu. Additional liver support avoids much of the usually encountered fatigue."
Aromatherapy Lifestyle: Science-Based Self Medicine with Essential Oils
An advanced aromatherapy course designed by Dr. rer. nat. Kurt Schnaubelt
Pacific Institute of Aromatherapy, 2004, page 60.

“Only when there is enough moisture, proper hormonal balance, and sufficient blood should a flushing out of the pathogenic factor be initiated. If the body is not sufficiently hydrated to support flushing, the healing crisis will be too strong and the patient will likely revert back to the vicious cycle of steroids and flare-ups. To determine whether the body is sufficiently hydrated, the presentation of lips and mouth (dry or moist), bronchi (dry or moist), and eyes and nose along with their associated mucous membranes is considered. Once the determination has been made to attempt elimination of the pathogenic factor, essential oils can be used to trigger wei qi. Depending on the condition, different essential oils may be appropriate.
- For metabolic conditions and to help elimination from liver and digestive tract: Rosemary verbenone
- To draw chronically lodged viruses from tissue or to draw a pathogenic factor from bones: Clove
- To draw biological pathogens or lactic acid from muscles and joints: Litsea cubeba, Lemon verbena, or Spruce
- To draw inorganic toxins such as uric acids and mineral-type deposits: Celery Seed (or Celery juice can also be effective)”
Schnaubelt Ph.D., Kurt (2011-11-08), The Healing Intelligence of Essential Oils: The Science of Advanced Aromatherapy, pages 194-195.

"Summing Up: When overwhelming stress depletes the blood, endocrine, and exocrine fluid resources of our body to the point that they become inadequate to support the complete elimination of a pathogenic factor, autoimmune disease is the result. Without the chance to fully eliminate the pathogenic factor, our immune system periodically attempts to resolve the condition. Considering that the pathogenic factor had taken up residency over long periods of time and created its own manifestations in the life of a human body, it is not too surprising that the elimination processes that are necessary to truly get rid of it sometimes take on dramatic forms."
Schnaubelt Ph.D., Kurt (2011-11-08), The Healing Intelligence of Essential Oils: The Science of Advanced Aromatherapy, page 195.

Chronic Fatigue Muscular Pain Oil from The Complete Aromatherapy & Essential Oils Handbook for Everyday Wellness by Purchon/Cantele

20 drops Bergamot
15 drops Marjoram
10 drops Ginger
5 drops Black Pepper

Combine 4 tsp (20mL) Grapeseed or Sweet Almond oil, 20 drops Borage seed oil and 8 drops Chronic Fatigue Muscular Pain Oil. Mix well and massage over the body.

[HEO’s Comment: If you don’t have these carrier oils, you can use what you have.]

Top Anti-inflammatory oils (from Higley's Reference Guide for Essential Oils)
Basil
Bergamot
German Chamomile
Myrrh
Spruce

Also consider:
Birch
Helichrysum
Hyssop
Lavender
Lavandin
Lemongrass
Peppermint
Pettitgrain
Spearmint
Spikenard
Tarragon
Idaho Tansy
Yarrow

Other helpful info:

This is an interesting case that emphasizes the importance of food sensitivities in autoimmune diseases like Hashimoto's: "This patient is a 61 year old female who was diagnosed with Scleroderma about 10 years ago. This is an autoimmune condition that affects soft tissue, especially in the fingers. She initially came into the office with "sausage fingers". They were really swollen, red and difficult to bend. She had been to a Rheumatologist who started her on a powerful immune suppressing medication called Plaquenil. However, the medication wasn't really helping. We did a food allergy panel and identified sensitivities to wheat and dairy. Since eliminating the foods, her fingers have now returned to normal. The thing that she really noticed was being able to wear her rings again. However, when she cheated and had some pizza her fingers got really red and swollen. Everyone with an autoimmune condition should consider having an IgG food allergy panel done.” - Dr. Wiggy: Thyroid MD

A Natural Perspective on Autoimmune Disorders by Michelle Newport, MH, NHC
Essential Oils that may be beneficial for autoimmune disorders include Bergamot, Clary Sage, Lavender and Roman Chamomile. Avoid essential oils that stimulate the immune system such as Geranium, Thyme and Ylang Ylang.

Autoimmune Diseases:
Alopecia Areata
Alzheimer's Disease
Celiac Disease
Crohn's Disease
Fibromyalgia
Graves Disease
Lupus
Multiple Sclerosis
Psoriasis
Rheumatoid Arthritis

The Wahls Protocol: How I Beat Progressive MS Using Paleo Principles and Functional Medicine by Terry Wahls, M.D. 

“You can arrest the development of autoimmune disease - which includes thyroid autoimmune disease - by healing the gut.”Dr. - Tom O’Bryan, author of The Autoimmune Fix

Autoimmunity and the Gut by Andrew W Campbell
"It is clear that the gut microbiota has a profound and long-term effect starting at birth on the host immune system. It is also evident that it plays a significant role in autoimmune diseases both inside and outside the gut."

Pantethine/Pantothenic Acid
"Pantethine is critical to the management of auto-immune disorders as well as adrenal fatigue. Pantethine allows the adrenal glands to generate more cortisone which is an anti-stress hormone. With more cortisone produced, the body's inflammatory response is reduced. For maximum effect, it should be used in conjunction with a high dose nutritional cocktail of vitamin C, lysine, proline, bioflavonoids, pine bark extract, glycine, carnitine, magnesium, frutooligosaccharides, glutamine, and ascorbyl palmitate.” - Dr. Lam

Rheumatoid arthritis affects both the bones and the surrounding tissue. It is an autoimmune disease, which means that the immune system begins attacking the body’s own tissues. Rheumatoid arthritis often destroys the bone surface, the cartilage, and the tissues surrounding the joint. Fluids accumulate and inflame the joints. The small joints of the ankles, feet, hands, knees, and wrists are most often affected, although rheumatoid arthritis can attack any joint in the body. It causes pain, stiffness, swelling, and sometimes disabling deformities. The exact cause or causes of most cases of rheumatoid arthritis are unknown. Researchers suspect that abnormal bowel function, food allergies, heredity, infections, nutritional deficiencies, and weakened immunity contribute. Another possibility is increased intestinal permeability, which allows bacterial toxins or tiny particles of undigested food to leak from the intestines into the bloodstream, where they can initiate an immune response. Foods that can trigger or aggravate arthritis in susceptible people include alcohol, corn, dairy products, sugar, and wheat. Members of the nightshade family— which includes potatoes, eggplant, peppers, tomatoes, and tobacco— may also promote joint inflammation and interfere with joint repair in some people.

Good nutrition can play a big role in controlling this disorder. A nutritionist or health-care professional can detect and help you correct any nutritional deficiencies. A low-fat, low-sugar diet centered on fresh vegetables and whole grains may provide relief. Some people find that avoiding citrus fruits, dairy products, processed and refined foods, red meat, salt, and sugar, as well as vegetables in the nightshade family, diminishes inflammation. Iron supplements can exacerbate arthritis, while flaxseed oil and garlic may bring relief. Physical therapy and exercise can maintain and restore muscle strength and, in some cases, can decrease symptoms. Aromatherapy complements other treatments for arthritis.

Wilson, Roberta, Aromatherapy: Essential Oils for Vibrant Health and Beauty, pages 174-175.