Associations have been shown between father’s absence and menarcheal age, but most studies have focused on absence resulting from divorce, abandonment or death. Little research has been conducted to evaluate the effect on menarcheal age of paternal absence through migrant work. In a sample of 400 middle school students, this study examined the association between paternal migrant work and menarcheal age against a backdrop of extensive rural-to-urban migration in China. Data were collected through a self-reported questionnaire, including social-demographic characteristics, aspects of family relationships, information about father’s migrant work and age at menarche. After adjusting for BMI, parent marital status and perceived relationship with mother, lower self-perceived quality of father–daughter relationship (both ‘father present, relationship poor’ and ‘father absent, relationship poor’) and lower frequency of contact with the father were associated with higher odds for early menarche. These findings suggest that the assumption that father’s absence for work influences the timing of menarche needs to be examined in the context of the quality of the father–daughter relationship and paternal care, which appear to play a critical role in the timing of menarche. These findings also emphasize the importance of enhancing paternal involvement and improving father–daughter relationships in the development of appropriate reproductive strategy in daughters.