Background Neonatal mortality due to preterm birth and low birthweight remains a significant challenge in Pakistan. Kangaroo mother care (KMC) is a unique, low-cost intervention proven to reduce neonatal mortality and morbidity and increase exclusive breastfeeding rates. However, KMC has not been attempted in community settings in Pakistan. We aim to implement and evaluate the effectiveness of a community-based KMC package to reduce neonatal morbidity and mortality among preterm and low birthweight (LBW) infants, which will provide evidence for policy development and the large-scale implementation of KMC across the country. Objective The primary objective of this trial is to reduce neonatal mortality among preterm and LBW infants. The secondary objectives are growth (measured as weight gain), reduced incidence of possible serious bacterial infection, and increased exclusive breastfeeding and continued breastfeeding practices. Methods We designed a community-based cluster randomized controlled trial in one rural district of Pakistan. Stable, LBW babies (weighing 1200 grams to 2500 grams) are included in the study. The community KMC package, consisting of the KMC kit, information and counseling material, and community mobilization through KMC champions (village volunteers), was designed after preliminary research in the same geographical location and implemented in intervention clusters. The standard essential newborn care is offered in the control clusters. Infants are recruited and followed up by independent teams of data collectors. Data are collected on the duration of skin-to-skin contact, growth, breastfeeding practices, morbidities, neonatal mortality, and neurodevelopment status. Data analysis will be conducted based on the intention to treat principle. The Cox regression model will be used to assess the primary outcome of neonatal mortality. The secondary outcomes will be evaluated using linear or logistic regression. Results The Ethics Review Committee of Aga Khan University, Pakistan, approved the study protocol in February 2017. Data collection began in August 2019 and will be completed in December 2021. Data analyses are yet to be completed. Conclusions This intervention may be effective in preventing sepsis and subsequently improve survival in LBW newborns in Pakistan and other low-income and middle-income countries worldwide. Trial Registration clinicaltrials.gov NCT03545204; https://clinicaltrials.gov/ct2/show/NCT03545204 International Registered Report Identifier (IRRID) DERR1-10.2196/28156