Abstract Background The prevalence of otitis media in Greenlandic children is one of the highest in the world. International studies have shown that otitis-prone children may benefit from tubulation of the tympanic membrane. However, it is unknown whether these results can be applied to Greenlandic children and trials on the effects of ventilation tubes in high-risk populations have, to our knowledge, never been conducted. Methods The trial is an investigator-initiated, multicentre, randomized, blinded superiority trial of bilateral ventilation tube insertion versus treatment as usual (no tube) in Greenlandic children aged 9–36 months with chronic otitis media with effusion or recurrent acute otitis media. With randomization stratified by otitis media subtype and trial site, a type 1 error of 5% and a power of 80%, a total of 230 participants are needed to detect a decrease of two visits to a health clinic during 2 years, which is considered the minimal clinical relevant difference. The primary outcome measure will be assessed blindly by investigating medical records. Secondary outcome measures are number of episodes of acute otitis media, quality of life, number of episodes of antibiotics administration and proportion of children with tympanic membrane perforations. Discussion This trial will provide evidence-based knowledge of the effects of ventilation tubes in children with middle ear infections from the high-risk Greenlandic population. Furthermore, this trial will improve the understanding of conducting randomized clinical trials in remote areas, where management of logistical aspects is particularly challenging. Trial registration ClinicalTrials.gov, NCT02490332 . Registered on 14 February 2016.