As with other hematological diseases treatment for acquired bone marrow aplasia combines directed treatment and support treatment.

- Support treatment: The aim of support treatment is to alleviate the patient's symptoms. In order to improve the manifestations deriving from the anemia, patients are administered a red blood cell transfusion. If there is secondary bleeding due to the lack of platelets, a platelet transfusion is administered. In cases where there is fever, a course of antibiotics is administered and, given that such patients have low defences, the necessary levels of hygiene must be observed to avoid further infections.

Patients with less severe aplasia may almost be asymptomatic and not require such support treatment.

- Directed treatment: In cases where the cause of the bone marrow aplasia has been established, the main treatment is to suppress the causal agent. Sometimes androgens (male hormones) are used to correct the aplasia, however, it must be borne in mind that these drugs might have significant side effects and are more effective in those aplasias associated with protein defects that keep the size of the chromosomes stable (telomerase). 

As mentioned at the beginning, acquired bone marrow aplasia presents secondary to an autoimmune mechanism and patients are treated with immunosuppressive drugs in association, on occasion, with a stem cell transplant.

Patients with less severe aplasia must be treated with an immunosuppressive agent called cyclosporin A in association, sometimes, with anti-thymocyte globulin (better known as ATG) and factors to stimulate hematopoiesis (such as G-CSF). Symptoms are resolved with this treatment for 50-60% of patients although, in a third of cases the aplasia may reappear after time, it being necessary to repeat the treatment.

The treatment of choice, for severe and very severe bone marrow aplasias for patients under the age of 40, is a bone marrow transplant from a sibling or histocompatible (HLA identical) non-related donor. With this procedure up to 90% of patients find a cure.

For older patients, or those who do not have an HLA compatible donor, treatment is based on the administration of anti-thymocyte globulin (ATG) in association with a cyclosporin A. These drugs resolve the aplasia in 50-70% of cases, although a third of patients will suffer a relapse some time afterwards and the responses achieved are mostly partial (the blood count does not return to normal). Although it is still pending authorisation by some health authorities, a recent study has observed that the addition of a drug to stimulate hematopoiesis (eltrombopag) at the beginning of treatment with ATG and cyclosporin A increases the number of global and complete responses. The worst responses are those of patients over 40 years of age with very severe aplasia. 

In cases of relapse, or if the patient does not respond to initial treatment, a second course of immunosuppressive treatment (30% response) should be considered, as should the administration of eltrombopag (45-50% response), or a bone marrow transplant if there is a haploidentical or compatible donor (related or non-related).

The long-term prognosis depends on the severity of the aplasia, the patient's age, earliness in starting the immunosuppressive treatment and the availability, or otherwise, of a compatible (related or non-related) donor. Two thirds of patients who receive immunosuppressive treatment are cured after one or two courses. With a bone marrow transplant the probability of a cure varies between 70-95% for transplants from compatible siblings, and 70-85% for transplants from non-related donors.