Household air pollution (HAP) mainly from cooking fuel is one of the major causes of respiratory illness and deaths among young children in low and middle-income countries like Pakistan. This study investigates for the first time the association between HAP from cooking fuel and under-five mortality using the 2013 Pakistan Demographic and Health Survey (PDHS) data. Multi-level logistic regression models were used to examine the association between HAP and under-five mortality in a total of 11,507 living children across four age-groups (neonatal aged 0–28 days, post-neonatal aged 1–11 months, child aged 12–59 months and under-five aged 0–59 months). Use of cooking fuel was weakly associated with total under-five mortality (OR = 1.22, 95%CI = 0.92–1.64, P = 0.170), with stronger associations evident for sub-group analyses of children aged 12–59 months (OR = 1.98, 95%CI = 0.75–5.25, P = 0.169). Strong associations between use of cooking fuel and mortality were evident (ORs >5) in those aged 12–59 months for households without a separate kitchen using polluting fuels, and in children whose mother never breastfed. The results of this study suggest that HAP from cooking fuel is associated with a modest increase in the risk of death among children under five years of age in Pakistan, but particularly in those aged 12–59 months, and those living in poorer socioeconomic conditions. To reduce exposure to cooking fuel which is a preventable determinant of under-five mortality in Pakistan, the challenge remains to promote behavioural interventions such as breastfeeding in infancy period, keeping young children away from the cooking area, and improvements in housing and kitchen design.