This study examined how fertilizer subsidy improves maize productivity in northern Ghana. The study, which involved 486 farmers, used an endogenous treatment effect model to measure the effect of subsidy participation on agricultural productivity. The results indicated that fertilizer subsidy increased the productivity of maize by 230.4 kg/acre. Farmers’ age, sex, access to extension services, farm size and farm income were the determinants of subsidy participation, while productivity was influenced by age, sex, household size, soil fertility status and farm income. The study calls for adopting pro-poor measures such as input subsidization, especially for smallholder farmers, to boost fertilizer use and farm productivity in low-income countries. The government of Ghana should, therefore, expand the subsidy programme to reach farmers who did not receive the subsidy. The study further recommends that farmers’ access to extension services should be enhanced since agricultural extension workers are pivotal to the implementation and success of the fertilizer subsidy programme. Also, subsidized fertilizer should be supplied to farmers on time to ensure effective utilization of the subsidy to increase productivity.