This study investigated the influence of climate factors on malaria incidence in the Sundargarh district, Odisha, India. The WEKA machine learning tool was used with two classifier techniques, Multi-Layer Perceptron (MLP) and J48, with three test options, 10-fold cross-validation, percentile split, and supplied test. A comparative analysis was carried out to ascertain the superior model among malaria prediction accuracy techniques in varying climate contexts. The results suggested that J48 had exhibited better skill than MLP with the 10-fold cross-validation method over the percentile split and supplied test options. J48 demonstrated less error (RMSE = 0.6), better kappa = 0.63, and higher accuracy = 0.71), suggesting it as most suitable model. Seasonal variation of temperature and humidity had a better association with malaria incidents than rainfall, and the performance was better during the monsoon and post-monsoon when the incidents are at the peak.