The gendered analysis of fertility as a migration factor is not a common perspective in migration studies, although in sub-Saharan African countries men and women are both involved in internal migration flows. The aim of this paper is to highlight how fertility factors (child's rank of birth, pregnancy and duration since birth) change internal migration behaviors. By using Event History Models of longitudinal data from urban and rural Health and Demographic Surveillance Sites (HDSS) in Burkina Faso, we analyze the effect of female fertility on male and female in-migration and outmigration in one rural HDSS (Nanoro) and one urban HDSS (Ouagadougou). The partner's migration status is included as a heterogeneity factor to explain both migrant and non-migrant migration behaviors. The results show a high selection effect of fertility among men and women in-migrating from the rural area to the urban area, and out-migrating from the urban and rural areas. Compared to those married to permanent residents, men and women married to migrants have higher chances of outmigrating if the partner is an HDSS resident. The first pregnancy exerted a boosting effect on female inmigration, fertility presents a mixed effect on male in-migration. The pregnancy and the child rearing have a delaying effect on both female and male out-migration.