In response to the perennial low harvest and high food prices, a number of Sub-Saharan African countries have instituted agricultural input subsidy programmes to increase food production and reduce poverty among small-scale farmers. Given that agriculture employs a large portion of working children on the continent, this paper studies the effect of these subsidy programmes on child labour. The paper analyses three rounds of the Malawi Integrated Household Panel Survey to answer the research question. The econometric results show that the farm input subsidy program in Malawi has a significant and positive impact on child labour in the country. The results suggest that in spite of the success of the programme in achieving its core aims, there are unintended negative consequences that could negatively affect human capital development. This could in turn adversely affect the ultimate poverty eradication efforts in the country and in the sub-region. To mitigate this problem, governments and implementing agencies should consider conditioning the distribution of the inputs on positive outcome like the school performance of the wards of beneficiaries.