Obstructive sleep apnea (OSA) is prevalent in patients with heart failure. Treatment with continuous positive airway pressure (CPAP) improves systolic function in patients with heart failure. Bilevel positive airway pressure (PAP) is another treatment modality for OSA. The intermediate-term effect of bilevel PAP on left ventricular ejection fraction (LVEF) in patients with stable heart failure and OSA has not been compared to the effect of CPAP. In this pilot randomized controlled trial, patients with stable systolic dysfunction and newly diagnosed OSA (n = 24) were randomized to receive either CPAP or bilevel PAP. Titration was done in the sleep laboratory using a CPAP-based algorithm. Primary outcome was the improvement in LVEF after 3 months of treatment. Other measurements included 6-min walk test, Epworth sleepiness scale score, and the Minnesota Living With Heart Failure questionnaire. Bilevel PAP increased LVEF 7.9% (LVEF percentage scale) more than CPAP (95% confidence interval [CI], 2.3 to 13.4; p = 0.01). In the bilevel PAP group, LVEF increased 8.5% (95% CI, 3.7 to 13.4; p = 0.002). In the CPAP group, LVEF did not change significantly (0.5%; 95% CI, - 2.7 to 3.7; p = 0.7). The difference in LVEF improvement between the two groups was still significant after adjustment for adherence, level of treatment positive pressure, body mass index, and severity of OSA. This pilot randomized controlled trial suggests that bilevel PAP is superior to CPAP in improving LVEF in patients with systolic dysfunction and OSA. Larger trials are required to evaluate the mechanism behind this effect.