Objective To determine whether there is an association between being smacked by your main caregiver in the first two years and emotional and behavioural problems at age four. Methods Design: Secondary analysis of data from the Growing Up in Scotland Prospective Study (GUS). Setting: Scotland, UK. Participants: GUS birth cohort children, whose main caregiver had no concerns about their behaviour at 22 months. Exposure: Ever smacked by main caregiver in first 22 months, as measured by caregiver self‐report at 22 months. Main Outcome: Emotional and behavioural problems as measured by parental assessment and the Strengths and Difficulties Questionnaire (SDQ) at 46 months. Results Preschool children exposed to main caregiver smacking in the first two years were twice as likely to have emotional and behavioural problems as measured by parental assessment [odds ratio (OR) 2.5, 95% confidence interval (CI) 1.9–3.2; absolute risk reduction (ARR) 17.8%, 95% CI 12.1–23.5] and SDQ (OR 2.5, 95% CI 1.7–3.7; ARR 7.5%, 95% CI 3.7–11.5), as children never smacked by their main caregiver. The association remained significant after adjusting for child age and sex, caregiver age, sex, ethnicity, educational attainment and mental health status, sibling number, structural family transitions and socioeconomic status (adj. OR 2.4, 95% CI 1.8–3.2 for parental assessment and adj. OR 2.2, 95% CI 1.4–3.5 for SDQ). Conclusions Parental use of physical punishment in the first two years may be a modifiable risk factor for emotional and behavioural difficulties in preschool children.