Since 2010, the Roll Back Malaria (RBM) Partnership, including National Malaria Control Programs, donor agencies (e.g., President's Malaria Initiative and Global Fund), and other stakeholders have been evaluating the impact of scaling up malaria control interventions on all-cause under-five mortality in several countries in sub-Saharan Africa. The evaluation framework assesses whether the deployed interventions have had an impact on malaria morbidity and mortality and requires consideration of potential nonintervention influencers of transmission, such as drought/floods or higher temperatures. Herein, we assess the likely effect of climate on the assessment of the impact malaria interventions in 10 priority countries/regions in eastern, western, and southern Africa for the President's Malaria Initiative. We used newly available quality controlled Enhanced National Climate Services rainfall and temperature products as well as global climate products to investigate likely impacts of climate on malaria evaluations and test the assumption that changing the baseline period can significantly impact on the influence of climate in the assessment of interventions. Based on current baseline periods used in national malaria impact assessments, we identify three countries/regions where current evaluations may overestimate the impact of interventions (Tanzania, Zanzibar, Uganda) and three countries where current malaria evaluations may underestimate the impact of interventions (Mali, Senegal and Ethiopia). In four countries (Rwanda, Malawi, Mozambique, and Angola) there was no strong difference in climate suitability for malaria in the pre- and post-intervention period. In part, this may be due to data quality and analysis issues.