Introduction: Individual, social and economic circumstances faced by young mothers can challenge a successful start in life for their children. Intervening early might enhance life chances for both mother and child. The Family Nurse Partnership (FNP) is an intensive nurse-led home visiting programme developed in the US which aims to improve prenatal health behaviours, birth outcomes, child development and health outcomes, and maternal life course. Establishing evidence of effectiveness beyond the original US setting is important to understand where further adaptation is required within a country specific context. Objective: This study will form one strand of the Scottish Governments? plan to evaluate the effectiveness of FNP as compared to usual care for mothers and their children in Scotland and will focus only on outcomes that can be identified using routine administrative data systems. Methods: This study is a natural experiment with a case-cohort design using linked anonymised routine health, educational and social care data. Cases will be women enrolled as FNP Clients in ten NHS Health Boards in Scotland and Controls will be women who met FNP eligibility criteria but were pregnant at a time when the programme was not recruiting. Outcomes are mapped to the Scottish FNP logic model. All comparative analyses will be pre-specified, conducted on an intention to treat basis and will use multilevel regression models to compare outcomes between groups. Discussion: The study protocol is based upon the specification of FNP commissioned by the Scottish Government. This study design is novel for the evaluation of the FNP/NFP programmes which are primarily evaluated with an RCT. Outcomes included within the study have been selected on the basis that they are outcomes FNP aims to influence and where there is routine data available to assess the outcome.