BackgroundIn many parts of the world, school-age children have high dental treatment needs; however, there is often low, or no, dental care provision. Although Atraumatic Restorative Treatment (ART) was developed to address this, its survival rate in occluso-proximal lesions is low. An alternative, the Hall Technique (HT) has shown better relative outcomes for occluso-proximal lesions, but has not been directly compared to ART or tested in field settings. This trial will compare ART and the HT for the most clinically- and cost-effective strategy for managing occluso-proximal lesions in primary molars, in a school setting, using low-technology and child-friendly dental techniques.Methods/DesignThis two-arm, parallel group, patient-randomized controlled, superiority trial will have treatment provided in schools. Schoolchildren (n = 124, age 6–8) with at least one occluso-proximal carious primary molar lesion will have random allocation to treatment with ART or HT. Baseline measures and outcome data will be assessed through participant report, clinical examination and parent report/questionnaires. The primary outcome is survival rate, a composite measure of absence of Minor Failures (a defect in the restoration/crown, but not interfering with tooth health) and Major Failures (signs or symptoms of irreversible pulp damage, such as dental fistula/abscess, tooth fracture or failures that cannot be repaired). Secondary outcomes are: (1) child-reported discomfort, (2) childrens’ and (3) parents’ concerns around dental appearance and (4) acceptability of treatments, (5) occlusal-vertical dimensions (OVD) changes, (6) plaque index, (7) gingival health, (8) decayed, missing, filled teeth in permanent teeth (DMFT)/decayed, missing, filled teeth in primary teeth (dmft), (9) oral health-related-quality of life, reported by children and parents/caregivers, (10) the incremental cost-effectiveness, and (11) operator effect. A trained and calibrated examiner will evaluate the treated teeth after 1 week, then 1, 6, 12, 24 and 36 months post treatment. Kaplan-Meier and Cox regression tests will be used to investigate the primary outcome. The Mann-Whitney or t test, Friedman test, paired t test or Wilcoxon test and Ordinal Logistic Regression Analysis will be used to analyze the secondary outcomes.DiscussionThe results of this trial will support decision-making by clinicians and policy-makers for managing occluso-proximal lesions in settings with constrained resources and limited dental access.Trial registrationwww.clinicaltrials.gov, NCT02569047, registered 5 October 2015.Electronic supplementary materialThe online version of this article (doi:10.1186/s13063-016-1270-z) contains supplementary material, which is available to authorized users.