Any stage of Lyme disease is treatable in almost all circumstances. Most people experience a full, quick recovery with minor complications. However, some people recover slowly if diagnosed when the disease is in its later stages.  Left untreated, Lyme disease can be permanently disabling or even fatal in some instances.

Lyme disease can be treated most effectively with minimal risk for further complications if diagnosed in its early stages. Antibiotics stop the disease from progressing and may lessen the severity of symptoms. Patients experiencing early-phase Lyme disease receive oral antibiotics daily for 10 to 14 days. In certain cases oral antibiotics may produce side effects such as upset stomach, diarrhea or allergic reaction.

Arthritis that is caused by Lyme disease (infectious arthritis) is also treated with antibiotic therapy. In some cases when arthritis lingers after antibiotic treatment, drugs that suppress inflammation may be required.

Late-stage, ongoing or serious Lyme disease usually requires intravenous (I.V.) antibiotics (e.g., ceftriaxone, cefotaxime). Through a catheter placed in a vein, antibiotics are administered daily for about two to four weeks. Side effects of I.V. antibiotics vary and may include a decrease in white blood cells, abdominal pain, diarrhea, colitis (inflammation of the colon) or allergic reaction.

People with Lyme disease may also need anti-inflammatory medication such as ibuprofen to reduce inflammation and pain and to improve function.

Patients receiving antibiotic treatment for Lyme disease sometimes experience a short–term worsening of symptoms (Jarisch-Herxheimer reaction) caused by dying bacteria. It typically begins about 24 hours after antibiotic treatment has begun and lasts about the same amount of time before ending. Antibiotics should continue to be administered as originally intended if a Jarisch-Herxheimer reaction occurs.  

In cases where antibiotic treatment shows no effect in an individual considered to have Lyme disease, re-evaluation by a physician is typically necessary. The most common reason for this occurrence is misdiagnosis, with symptoms attributed to Lyme disease actually being caused by another condition.

Patients are urged not to try unproven, unapproved and possibly dangerous substances that are sometimes touted as a cure for Lyme disease. The U.S. Food and Drug Administration in 2006 issued a warning against an injected compound called bismacine or chromacine. It can cause complications including kidney failure and cardiovascular collapse and is blamed for at least one death.

The Infectious Diseases Society of America (IDSA) updated its guidelines on Lyme disease in 2006. Its general recommendations include:

• Not routinely using antibiotics after a tick bite
  
  
• Offering one oral dose of the antibiotic doxycycline only in specific circumstances for people who were bitten by a tick but do not show symptoms of the disease
  
  
• Treating early Lyme disease with oral doxycycline, amoxicillin or cefuroxime axetil
  
  
• Avoiding doxycycline in pregnant patients
  
  
• Treating early neurologic Lyme disease (involving meningitis or radiculopathy) with intravenous ceftriaxone
  
  
• Treating late neurologic Lyme disease with intravenous ceftriaxone or, as an alternative, intravenous cefotaxime or penicillin G
  
  
• Not using certain treatments described as lacking in scientific evidence, such as hyperbaric (high-pressure) oxygen, ozone, fever therapy, certain dietary supplements, long-term use of antibiotics, combinations of antimicrobials, pulsed dosing, first-generation cephalosporins, fluoroquinolones, carbapenems, vancomycin, metronidazole, tinidazole, amantadine, ketolides, isoniazid, trimethoprim-sulfamethoxazole, fluconazole or benzathine penicillin G
  
  
• Using antimicrobials to treat the other diseases spread by the Lyme disease tick: human granulocytic anaplasmosis (HGA) and babesiosis. Doxycycline is suggested for all symptomatic patients suspected of having HGA. A combination of atovaquone and azithromycin, or clindamycin and quinine, is suggested for patients with active babesiosis.

The guidelines emphasize that they do not apply in all cases and are not meant to replace a physician's recommendations. They also stress the importance of preventing Lyme disease by reducing exposure to ticks.

The IDSA's recommendations have sparked some controversy, including criticism from the Lyme Disease Association that the opposition to long-term antibiotic therapy was depriving chronic Lyme patients of beneficial treatment. The International Lyme and Associated Disease Society (ILADS) recommends that antibiotic treatment be guided by the patient's response rather than preset limits, and says that for persistent Lyme disease a patient may need to be treated for months after symptoms have disappeared.