It has been known that second-hand smoking and deprivation could cluster together affecting child health. However, little is known on the role of household smoking rules. Therefore, it was aimed to study the relationships among indoor second-hand smoking, household smoking rules, deprivation level and children mental health in a country-wide and population-based setting. Data was retrieved from and analysed in Scottish Health Survey, 2013. Information on demographics, indoor second-hand smoking status, household smoking rules, deprivation level and child mental health by Strengths and Difficulties Questionnaire was obtained by household interview through parents. Statistical analysis included chi-square test and survey-weighted logistic regression modelling. Of 1019 children aged 4-12, 17.9% (n = 182) lived in the 15% most deprivation areas. Deprived areas tended to be where indoor smoking occurred (p < 0.001). The top three sub-regions of the 15% most deprivation for Scottish children are greater Glasgow, Ayrshire & Arran and Forth Valley while the top three sub-regions of exposure to the indoor second-hand smoking are Fife, Forth Valley and Ayrshire & Arran. The top three sub-regions with indoor smoking allowed are greater Glasgow, Western Isles and Borders. Children emotional and behavioural problems were reduced when the strict household smoking rules (not allowed or outdoor areas) applied. One in six Scottish children lived in the 15% most deprivation areas and exposed to indoor second-hand smoking that could have led to emotional and behavioural problems. Public health programs promoting strict household smoking rules should be encouraged in order to optimise children mental health.