Multipanel images, commonly seen as web screenshots, posters, etc., pervade our daily lives. These images, characterized by their composition of multiple subfigures in distinct layouts, effectively convey information to people. Toward building advanced multimodal AI applications, such as agents that understand complex scenes and navigate through webpages, the skill of multipanel visual reasoning is essential, and a comprehensive evaluation of models in this regard is important. Therefore, we introduce Multipanel Visual Question Answering (MultipanelVQA), a novel benchmark comprising 6,600 triplets of questions, answers, and multipanel images that specifically challenge models in comprehending multipanel images. Our evaluation shows that questions in the MultipanelVQA benchmark pose significant challenges to the state-of-the-art Multimodal Large Language Models (MLLMs) tested, even though humans can attain approximately 99% accuracy on these questions. Distinctively, the MultipanelVQA benchmark features synthetically generated multipanel images specifically crafted to isolate and assess the impact of various factors, such as the layout, on MLLMs’ multipanel image comprehension abilities. As a result, in addition to benchmarking the capabilities of MLLMs in understanding multipanel images, we analyze various factors of the multipanel image that affect MLLMs’ performance with synthetic data and offer insights for enhancement.