The Great Pyramid, or Khufu’s Pyramid, was built on the Giza plateau in Egypt during the fourth dynasty by the pharaoh Khufu (Cheops), who reigned from 2509 BC to 2483 BC. Despite being one of the oldest and largest monuments on Earth, there is no consensus about how it was built. To understand its internal structure better, we imaged the pyramid using muons, which are by-products of cosmic rays that are only partially absorbed by stone. The resulting cosmic-ray muon radiography allows us to visualize the known and any unknown voids in the pyramid in a non-invasive way. Here we report the discovery of a large void (with a cross-section similar to that of the Grand Gallery and a minimum length of 30 metres) situated above the Grand Gallery. This constitutes the first major inner structure found in the Great Pyramid since the nineteenth century. The void, named ScanPyramids’ Big Void, was first observed with nuclear emulsion films installed in the Queen’s chamber, then confirmed with scintillator hodoscopes set up in the same chamber and finally re-confirmed with gas detectors outside the pyramid. This large void has therefore been detected with high confidence by three different muon detection technologies and three independent analyses. These results constitute a breakthrough for the understanding of the internal structure of Khufu’s Pyramid. Although there is currently no information about the intended purpose of this void, these findings show how modern particle physics can shed new light on the world’s archaeological heritage.