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Background: Although mortality rates have declined in Uganda over the last decade, maternal mortality is still high at 336 deaths per 100,000 live births, as is infant mortality at 43 deaths per 1000 live births. One in every 19 babies born in Uganda does not live to celebrate their first birthday. Many of these deaths occur within the first 28 days of life, forming the single largest category of death. Promising effects for preventing death are expected from timed and targeted counselling (ttC), an intervention package of key messages and actions that address integrated health and nutrition needs of the mothers and children, barriers and negotiation agreement, to cause sustainable behavioural change at specific timelines in the first 1000 days., Methods: The study has a quasi-experimental design in order to evaluate the implementation and effectiveness of the ttC intervention. Participants are pregnant women who have been registered by village health team (VHT) members and who live in Hoima (intervention region) or Masindi (control region) districts, who will be monitored throughout their pregnancy up to at least six weeks after delivery. A multi-stage sampling technique will be employed to select participants, the study sites being purposively chosen. Sample size is determined using the pregnancy rate from the population estimates, resulting in a total required sample of 1218 (609 each in the intervention and control group). Study instruments that will be used include the Ugandan VHT household register (in which all mothers to be studied will be registered), the ttC register (an additional tool for the study area), and a study questionnaire, to collect data at outcome level. Univariate, bivariate and multivariate analyses will be performed using SPSS to evaluate intervention effects on outcomes (e.g., relationship between pregnancy outcomes and antenatal attendance). In addition, quantitative findings will be triangulated with qualitative data, and collected through interviews and focus group discussions with participants and implementers., Discussion: The proposed study will examine the effectiveness of implementing ttC to improve maternal and child outcomes in Uganda. If ttC is effective, broader implementation of appropriate antenatal services can be advised as essential newborn care improvements., Trial Registration: PACTR, PACTR202002812123868. Registered on 25 February 2020.