Background: This paper presents the study protocol for a pragmatic cluster randomized controlled trial (RCT) with a supplementary matched control group. The aim of the trial is to evaluate a community-based early education and development program launched by the Government of Indonesia. The program was developed in collaboration with the World Bank with a total budget of US$127.7 million, and targets an estimated 738,000 children aged 0 to 6 years living in approximately 6,000 poor communities. The aim of the program is to increase access to early childhood services with the secondary aim of improving school readiness.Methods/Design: The study is being conducted across nine districts. The baseline survey contained 310 villages, of which 100 were originally allocated to the intervention arm, 20 originally allocated to a 9-month delay staggered start, 100 originally allocated to an 18-month delay staggered start and 90 allocated to a matched control group (no intervention). The study consists of two cohorts, one comprising children aged 12 to 23 months and the other comprising children aged 48 to 59 months at baseline. The data collection instruments include child observations and task/game-based assessments as well as a questionnaire suite, village head questionnaire, service level questionnaires, household questionnaire, and child caretaker questionnaire. The baseline survey was conducted from March to April 2009, midline was conducted from April to August 2010 and endline conducted early 2013. The resultant participation rates at both the district and village levels were 90%. At the child level, the participation rate was 99.92%. The retention rate at the child level at midline was 99.67%.Discussion: This protocol paper provides a detailed record of the trial design including a discussion regarding difficulties faced with compliance to the randomization, compliance to the dispersion schedule of community block grants, and procurement delays for baseline and midline data collections. Considering the execution of the program and the resultant threats to the study, we discuss our analytical plan and intentions for endline data collection.Trials registration: Current Controlled Trials ISRCTN76061874. © 2013 Pradhan et al.; licensee BioMed Central Ltd.