The desire for children could be considered a reliable predictor of subsequent fertility. At the same time, the sex composition of surviving children, along with other demographic and socioeconomic factors, may affect a couple’s fertility desire and, therefore, their subsequent fertility. This study examined the impact of the sex composition of living children and a couple’s agreement on fertility desire on their subsequent fertility in India using data came from two rounds of nationally representative surveys: the India Human Development Survey (IHDS)-I (2004–05) and IHDS-II (2011–12). To understand which factors affect the chances of an additional pregnancy or childbirth, a random effects logistic regression model was applied to the panel data. It was found that the fertility desires of both marital partners were important in determining the chances of subsequent fertility. About 35% of the couples wanting to limit children had undergone pregnancy or childbirth, while 76% of the couples wanting more children had conceived or given birth to children. In the case of discordance between the spouses, subsequent fertility was found to remain intermediate between those agreeing to continue childbirth and those wanting to limit it. The findings also affirmed that child sex preference, specifically son preference, still persists in Indian society. More than 80% of the couples with only daughters in IHDS-I mutually wanted to have additional children, whereas in families that only had sons, the chance of a subsequent pregnancy was inversely associated with the number of sons. Strong patriarchal settings, combined with cultural and socioeconomic factors, affect the persistence of sex preference in India. Programmes aimed at increasing family planning use need to address son preference and should include components that promote the value of girl children.