Background Malaria has been one of the commonest diseases during farming season which affects farmers’ health resulting in number of days spend on the farm. Due to this, farmers always try to prevent malaria attack by averting. Motivated by this argument, this study sought to determine the effects of malaria averting expenditure on labour productivity of maize farmers in Bunkpurugu-Nakpanduri District in the Northern Region of Ghana.Methods A cross sectional primary data was collected from 194 maize farmers. Both descriptive and quantitative data analysis approaches were employed. Conditional Mixed Process was used to estimate the effects of malarial averting expenditure on maize labour productivity.Results The study revealed that maize farmers incurred an average averting expenditure amount of GH¢ 284.60 on malaria. The result shows that factors that significantly affect maize farmers averting expenditure include; households’ off-farm income, household size, presence of bushes around houses, presence of pregnant women and number of household members in school. Meanwhile, quantity of fertilizer, seed, weedicides, farming experience, age, ownership of motor bike and averting expenditure are significant determinants of maize labour productivity. The study revealed that as farmers spend more to avert malaria attack, the become more productive.Conclusions Therefore, this study recommends that Ministry of Health should increase a public advocacy to ensure a holistic approach on use of malaria averting strategies such as clearing of bushes around houses, draining of stagnant water, sleeping in treated mosquito nets among others.