BackgroundTo determine the effects of noninvasive mechanical ventilation (NIV) compared with invasive mechanical ventilation (IMV) as the initial mechanical ventilation on clinical outcomes when used for treatment of acute respiratory failure (ARF) in immunocompromised patients.MethodsWe searched PubMed, EMBASE, the Cochrane Central Register of Controlled Trials (CENTRAL), the Chinese Biomedical Literature Database (CBM) and other databases. Subgroup analyses by disease severity and causes of immunodeficiency were also conducted.ResultsThirteen observational studies with a total of 2552 patients were included. Compared to IMV, NIV was shown to significantly reduce in-hospital mortality (OR 0.43, 95 % CI 0.23 to 0.80, P value = 0.007) and 30-day mortality (OR 0.34, 95 % CI 0.20 to 0.61, P value < 0.0001) in overall analysis. Subgroup analysis showed NIV had great advantage over IMV for less severe, AIDS, BMT and hematological malignancies patients in reducing mortality and duration of ICU stay.ConclusionsThe overall evidence we obtained shows NIV does more benefits or at least no harm to ARF patients with certain causes of immunodeficiency or who are less severe.Electronic supplementary materialThe online version of this article (doi:10.1186/s12890-016-0289-y) contains supplementary material, which is available to authorized users.