BACKGROUND Unipolar depression is one of the most important mental disorders. Insomnia is a symptom of cardinal importance in depression. It increases the risk to develop depression, negatively affects disease trajectory, is the most common symptom after remission, increases the risk of relapse, and is associated with higher suicide rates. Existing therapies for insomnia in depression have limitations. Further adjuvant therapies are therefore needed. Acute aerobic exercise has been shown to have beneficial effects on sleep in healthy individuals and patients with insomnia. We therefore hypothesize that a single session of aerobic exercise has a positive impact on sleep in patients with unipolar depression. This trial aims to investigate the effects of a single bout of aerobic exercise on the subsequent night's sleep in patients with depression. METHODS This is a two-arm parallel group, randomized, outcome assessor blinded, controlled, superiority trial. Patients between 18 and 65 years of age with a primary diagnosis of unipolar depression (without a psychotic episode) are included. Exclusion criteria are regular use of hypnotic agents, opioids, and certain beta-blockers, as well as the presence of factors precluding exercise, history of epilepsy, restless legs syndrome, moderate obstructive sleep apnea, and a BMI > 40. The intervention is a single bout of aerobic exercise, performed for 30 min on a bicycle ergometer at 80% individual anaerobic threshold. The control group sits and reads for 30 min. The primary outcome is sleep efficiency measured by polysomnography. Secondary outcomes include further polysomnographic variables, subjective pre-sleep arousal, nocturnal cardiovascular autonomic modulation, subjective sleep quality, daytime sleepiness, and adverse events. According to the sample size calculation, a total of 92 patients will be randomized using minimization. CONCLUSIONS This trial will add new information to the body of knowledge concerning the treatment of insomnia in patients with depression. Thereby, the results will inform decision makers on the utility of acute aerobic exercise. BACKGROUND Clinicaltrials.gov, NCT03673397 . Protocol version 1 registered on 17 September 2018.