BACKGROUND: There are 2.5 million neonatal deaths each year; the majority occur within 48 h of birth, before stabilisation. Evidence from 11 trials shows that kangaroo mother care (KMC) significantly reduces mortality in stabilised neonates; however, data on its effect among neonates before stabilisation are lacking. The OMWaNA trial aims to determine the effect of initiating KMC before stabilisation on mortality within seven days relative to standard care. Secondary objectives include exploring pathways for the intervention's effects and assessing incremental costs and cost-effectiveness between arms. METHODS: We will conduct a four-centre, open-label, individually randomised, superiority trial in Uganda with two parallel groups: an intervention arm allocated to receive KMC and a control arm receiving standard care. We will enrol 2188 neonates (1094 per arm) for whom the indication for KMC is 'uncertain', defined as receiving ≥ 1 therapy (e.g. oxygen). Admitted singleton, twin and triplet neonates (triplet if demise before admission of ≥ 1 baby) weighing ≥ 700-≤ 2000 g and aged ≥ 1-< 48 h are eligible. Treatment allocation is random in a 1:1 ratio between groups, stratified by weight and recruitment site. The primary outcome is mortality within seven days. Secondary outcomes include mortality within 28 days, hypothermia prevalence at 24 h, time from randomisation to stabilisation or death, admission duration, time from randomisation to exclusive breastmilk feeding, readmission frequency, daily weight gain, infant-caregiver attachment and women's wellbeing at 28 days. Primary analyses will be by intention-to-treat. Quantitative and qualitative data will be integrated in a process evaluation. Cost data will be collected and used in economic modelling. DISCUSSION: The OMWaNA trial aims to assess the effectiveness of KMC in reducing mortality among neonates before stabilisation, a vulnerable population for whom its benefits are uncertain. The trial will improve understanding of pathways underlying the intervention's effects and will be among the first to rigorously compare the incremental cost and cost-effectiveness of KMC relative to standard care. The findings are expected to have broad applicability to hospitals in sub-Saharan Africa and southern Asia, where three-quarters of global newborn deaths occur, as well as important policy and programme implications. TRIAL REGISTRATION: ClinicalTrials.gov, NCT02811432. Registered on 23 June 2016.