Background The aim of this study is to assess if peer counseling of women improves breastfeeding, complementary feeding practices, and child growth, and thus reduces the prevalence of undernutrition in children up to 4 years of age. Objective Lack of exclusive breastfeeding and inappropriate complementary feeding are critical factors in reducing child undernutrition, morbidity, and mortality. There are reported trials of peer counseling to improve breastfeeding; however, they did not examine the efficacy of peer counseling to improve complementary feeding or the long-term impacts on child growth and development. Methods This study has used a community-based, cluster-randomized controlled trial with a superiority design and 2 parallel treatment arms. It is assessing the impact of peer counseling, starting in late pregnancy up to 1 year after delivery, on child feeding practices, growth, and development with follow-up until 48 months of age. The study site was Mirpur, a densely populated area in Dhaka. Using satellite maps and geographic information system mapping, we constructed 36 clusters with an average population of 5000 people. We recruited pregnant women in the third trimester aged 16-40 years, with no more than 3 living children. Trained peer counselors visited women at home twice before delivery, 4 times in the first month, monthly from 2 to 6 months, and again at 9 and 12 months. Trained research assistants collected anthropometric measurements. The primary outcome will be differences in child stunting and mean length for age at 6, 12, 15, and 18 months. Secondary outcomes will be differences in the percentage of women exclusively breastfeeding in the mean duration of any breastfeeding and in the percentage of children at 6 and 9 months of age who receive solid, semisolid, or soft foods; and the percentage of children consuming foods from 4 or more food groups at 9, 12, 15, and 18 months. We will assess the mean cognitive function scores from the Ages and Stages Questionnaire (9 and 18 months) and Bayley tests (24 and 36 months). Results We identified 65,535 people in mapped residences, from which we defined 36 clusters and randomly allocated them equally to intervention or control groups stratified by cluster socioeconomic status. From July 2011 to May 2013, we identified 1056 pregnant women and 993 births in the intervention group and 994 pregnancies and 890 births in the control group. At 18 months, 692 children remained in the intervention group and 551 in the control group. From January 2015 to February 2017, we conducted the long-term follow-up of the cohort. We have now completed the data collection and processing and have started analyses. Conclusions This study will help fill the evidence gap about the short- and long-term impact of peer counseling on improving infant feeding, preventing childhood undernutrition, and enhancing child cognitive development. Trial Registration ClinicalTrials.gov NCT01333995; https://clinicaltrials.gov/ct2/show/NCT01333995 International Registered Report Identifier (IRRID) DERR1-10.2196/31475