Abstract Background Interventions promoting optimal infant and young child nutrition could prevent a fifth of under-5 deaths in countries with high mortality. Poor infant and young child feeding practices are widely documented in Kenya, with potential detrimental effects on child growth, health and survival. Effective strategies to improve these practices are needed. This study aims to pilot implementation of the Baby Friendly Community Initiative (BFCI), a global initiative aimed at promoting optimal infant and young child feeding practices, to determine its feasibility and effectiveness with regards to infant feeding practices, nutrition and health outcomes in a rural setting in Kenya. Methods The study, employing a cluster-randomized trial design, will be conducted in rural Kenya. A total of 12 clusters, constituting community units within the government’s Community Health Strategy, will be randomized, with half allocated to the intervention and the other half to the control arm. A total of 812 pregnant women and their respective children will be recruited into the study. The mother-child pairs will be followed up until the child is 6 months old. Recruitment will last approximately 1 year from January 2015, and the study will run for 3 years, from 2014 to 2016. The intervention will involve regular counseling and support of mothers by trained community health workers and health professionals on maternal, infant and young child nutrition. Regular assessment of knowledge, attitudes and practices on maternal, infant and young child nutrition will be done, coupled with assessment of nutritional status of the mother-child pairs and morbidity for the children. Statistical methods will include analysis of covariance, multinomial logistic regression and multilevel modeling. The study is funded by the NIH and USAID through the Program for Enhanced Research (PEER) Health. Discussion Findings from the study outlined in this protocol will inform potential feasibility and effectiveness of a community-based intervention aimed at promoting optimal breastfeeding and other infant feeding practices. The intervention, if proved feasible and effective, will inform policy and practice in Kenya and similar settings, .